Installed a fresh SEPM on a server and after some use either the java console freezes or I get a failed to authenticate error message. The only to fix this seems to be restarting the SEPM service but this doesn't always work. As a result of this the event log has the good old "Java Virtual Machine has exited with a code of 1, the service is being stopped" with a source of semsrv and an event Id of 4096.
I have tried a repair install, changed the permissions of the relevant folders, changed the identity on the DefaultAppPool to Local System and none of this has seemed to help.
Running 11.0.6005.562 on Windows 2003 SP 2 Standard. I have pushed out a couple of clients and they have the little green icon over the systray icon so that means they can connect to SEPM. Also when using SEPM I have no issues (apart from it being a bit slow) however when I ran the Symantec Endpoint Protection Support Tool v1.0.5050 it reported 1 error:
Below is the catalina.out from the server...no idea if you need this to debug but it seems that everybody includes this when reporting the kind of problems I'm having. Either that or it's because catalina.out is cool 
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30-Jun-2011 09:07:41 org.apache.coyote.http11.Http11BaseProtocol init
INFO: Initializing Coyote HTTP/1.1 on http-9090
30-Jun-2011 09:07:44 org.apache.coyote.http11.Http11BaseProtocol init
INFO: Initializing Coyote HTTP/1.1 on http-8443
Starting service SCM
Apache Tomcat/4.1.39
Has valid SAV license
Info>> No SNAC license file in C:\Program Files\Symantec\Symantec Endpoint Protection Manager\tomcat\etc\license
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: ================== Server Environment ===================
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: os.name = Windows 2003
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: os.version = 5.2
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: os.arch = x86
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: java.version = 1.6.0_14
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: java.vendor = Sun Microsystems Inc.
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: java.vm.name = Java HotSpot(TM) Server VM
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: java.vm.version = 14.0-b16
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: java.home = C:\Program Files\Symantec\Symantec Endpoint Protection Manager\jdk\jre
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: catalina.home = C:\Program Files\Symantec\Symantec Endpoint Protection Manager\tomcat
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: java.user = null
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: user.language = en
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: user.country = GB
30-Jun-2011 09:07:53 com.sygate.scm.server.util.ServerLogger writeHeader
SEVERE: scm.server.version = 11.0.6005.562
30-Jun-2011 09:08:01 org.apache.commons.digester.Digester error
SEVERE: Parse Error at line 162 column 11: The content of element type "web-app" must match "(icon?,display-name?,description?,distributable?,context-param*,filter*,filter-mapping*,listener*,servlet*,servlet-mapping*,session-config?,mime-mapping*,welcome-file-list?,error-page*,taglib*,resource-env-ref*,resource-ref*,security-constraint*,login-config?,security-role*,env-entry*,ejb-ref*,ejb-local-ref*)".
org.xml.sax.SAXParseException: The content of element type "web-app" must match "(icon?,display-name?,description?,distributable?,context-param*,filter*,filter-mapping*,listener*,servlet*,servlet-mapping*,session-config?,mime-mapping*,welcome-file-list?,error-page*,taglib*,resource-env-ref*,resource-ref*,security-constraint*,login-config?,security-role*,env-entry*,ejb-ref*,ejb-local-ref*)".
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.error(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
at org.apache.xerces.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.commons.digester.Digester.parse(Digester.java:1745)
at org.apache.catalina.startup.ContextConfig.applicationConfig(ContextConfig.java:221)
at org.apache.catalina.startup.ContextConfig.start(ContextConfig.java:580)
at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:182)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:3644)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1148)
at org.apache.catalina.core.StandardHost.start(StandardHost.java:697)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1148)
at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:311)
at org.apache.catalina.core.StandardService.start(StandardService.java:450)
at org.apache.catalina.core.StandardServer.start(StandardServer.java:2213)
at org.apache.catalina.startup.Catalina.start(Catalina.java:484)
at org.apache.catalina.startup.Catalina.execute(Catalina.java:371)
at org.apache.catalina.startup.Catalina.process(Catalina.java:134)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:151)
[TraceMgr] Opening log file C:\Program Files\Symantec\Symantec Endpoint Protection Manager\tomcat/logs\ajaxswing.log
java.io.EOFException: Unexpected end of ZLIB input stream
at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:223)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:141)
at java.util.zip.ZipInputStream.read(ZipInputStream.java:146)
at com.sygate.scm.util.ZipUtil.unzipFromInputStream(ZipUtil.java:383)
at com.sygate.scm.util.ZipUtil.unzipFile(ZipUtil.java:296)
at com.sygate.scm.util.ZipUtil.unzipFile(ZipUtil.java:271)
at com.sygate.scm.server.task.PackageTask.upzipPackageToFullFolder(PackageTask.java:868)
at com.sygate.scm.server.task.PackageTask.updateIdcSettingEx(PackageTask.java:811)
at com.sygate.scm.server.task.PackageTask.updateIdcPackageSetting(PackageTask.java:763)
at com.sygate.scm.server.task.PackageTask.updateIdcSetting(PackageTask.java:736)
at com.sygate.scm.server.task.PackageTask.publishPackages(PackageTask.java:682)
at com.sygate.scm.server.task.PackageTask.run(PackageTask.java:303)
at java.util.TimerThread.mainLoop(Timer.java:512)
at java.util.TimerThread.run(Timer.java:462)
java.lang.ClassNotFoundException: com.sygate.scm.util.i18n.ErrorMsg_en_GB
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1541)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1386)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:169)
at com.sygate.scm.util.ErrorMsg.setLocale(ErrorMsg.java:229)
at com.sygate.scm.util.ErrorMsg.<clinit>(ErrorMsg.java:222)
at com.sygate.scm.server.util.ServerException.getMessage(ServerException.java:47)
at com.sygate.scm.server.task.PackageTask.run(PackageTask.java:321)
at java.util.TimerThread.mainLoop(Timer.java:512)
at java.util.TimerThread.run(Timer.java:462)
Exception in thread "Timer-6" java.lang.OutOfMemoryError: Java heap space
2011/06/30 09:24:05:687 : Thread-16 : [com.creamtec.ajaxswing.core.ClientAgentFactory$1] Exception while warming up client agent for applicaton sepm (Exception java.lang.OutOfMemoryError, Java heap space)
2011/06/30 09:24:06:859 : [com.creamtec.ajaxswing.core.ClientAgentFactory$1] Exception while warming up client agent for applicaton sepm
java.lang.OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space
2011/06/30 09:24:27:328 : Thread-16 : [com.creamtec.ajaxswing.core.ClientAgentFactory$1] Exception while warming up client agent for applicaton sepm (Exception java.lang.OutOfMemoryError, Java heap space)
2011/06/30 09:24:31:265 : [com.creamtec.ajaxswing.core.ClientAgentFactory$1] Exception while warming up client agent for applicaton sepm
java.lang.OutOfMemoryError: Java heap space
java.lang.OutOfMemoryError: Java heap space
Exception in thread "RMI TCP Connection(idle)" java.lang.OutOfMemoryError: Java heap space
Exception in thread "RMI TCP Connection(idle)" java.lang.OutOfMemoryError: Java heap space
Exception in thread "RMI TCP Connection(idle)" java.lang.OutOfMemoryError: Java heap space
Exception in thread "RMI TCP Connection(idle)" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Timer-1" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Timer-0" java.lang.OutOfMemoryError: Java heap space
2011/06/30 09:26:57:093 : Thread-16 : [com.creamtec.ajaxswing.core.ClientAgentFactory$1] Exception while warming up client agent for applicaton sepm (Exception com.creamtec.ajaxswing.core.AjaxSwingException, Timed out while waiting for a new JVM process. Possible reasons are:<ul><li> Application classes are not not found<li> JAVA_HOME environment variable is not set correctly (see AjaxSwing/bin/setEnv.bat)<li> AJAXSWING_HOME environment variable is not set correctly (see AjaxSwing/bin/setEnv.bat)<li> System configuration prevents AjaxSwing Router from launching agent process<li> The timeout value for router.agentWaitTimeout in default.properties is too low</ul>Check AjaxSwing log files for application errors.<br>Double check that you have made your classes available to AjaxSwing and that you can run AjaxSwing/bin/clientagent[.bat] with correct parameters manually)
2011/06/30 09:26:57:093 : [com.creamtec.ajaxswing.core.ClientAgentFactory$1] Exception while warming up client agent for applicaton sepm
com.creamtec.ajaxswing.core.AjaxSwingException: Timed out while waiting for a new JVM process. Possible reasons are:<ul><li> Application classes are not not found<li> JAVA_HOME environment variable is not set correctly (see AjaxSwing/bin/setEnv.bat)<li> AJAXSWING_HOME environment variable is not set correctly (see AjaxSwing/bin/setEnv.bat)<li> System configuration prevents AjaxSwing Router from launching agent process<li> The timeout value for router.agentWaitTimeout in default.properties is too low</ul>Check AjaxSwing log files for application errors.<br>Double check that you have made your classes available to AjaxSwing and that you can run AjaxSwing/bin/clientagent[.bat] with correct parameters manually
at com.creamtec.ajaxswing.core.JVMFactory.waitForJVM(JVMFactory.java:194)
at com.creamtec.ajaxswing.core.JVMFactory.launchJVM(JVMFactory.java:123)
at com.creamtec.ajaxswing.core.JVMFactory.getAvailableJVM(JVMFactory.java:62)
at com.creamtec.ajaxswing.core.ClientAgentFactory.createNewAgent(ClientAgentFactory.java:241)
at com.creamtec.ajaxswing.core.ClientAgentFactory$1.run(ClientAgentFactory.java:168)
com.creamtec.ajaxswing.core.AjaxSwingException: Timed out while waiting for a new JVM process. Possible reasons are:<ul><li> Application classes are not not found<li> JAVA_HOME environment variable is not set correctly (see AjaxSwing/bin/setEnv.bat)<li> AJAXSWING_HOME environment variable is not set correctly (see AjaxSwing/bin/setEnv.bat)<li> System configuration prevents AjaxSwing Router from launching agent process<li> The timeout value for router.agentWaitTimeout in default.properties is too low</ul>Check AjaxSwing log files for application errors.<br>Double check that you have made your classes available to AjaxSwing and that you can run AjaxSwing/bin/clientagent[.bat] with correct parameters manually
at com.creamtec.ajaxswing.core.JVMFactory.waitForJVM(JVMFactory.java:194)
at com.creamtec.ajaxswing.core.JVMFactory.launchJVM(JVMFactory.java:123)
at com.creamtec.ajaxswing.core.JVMFactory.getAvailableJVM(JVMFactory.java:62)
at com.creamtec.ajaxswing.core.ClientAgentFactory.createNewAgent(ClientAgentFactory.java:241)
at com.creamtec.ajaxswing.core.ClientAgentFactory$1.run(ClientAgentFactory.java:168)