Hello,
If your users are seeing the Active Scan popup when they logon, then you likely have Show Scan Progress selected in the Virus and Spyware Policy. You could either change this so that scan progress is hidden (the users would not see any popups) or you could disable Startup Scans.
Hiding scan progress
- Login to the SEPM
- Click Clients
- Select your group which is affected by this issue
- Click the Policies tab (at the top)
- Open your Virus and Spyware Protection policy
- Click Administrator-Defined Scans
- Click Advanced
- Under Show scan pgoress options, select Do not show scan progress.
- Click OK.
- Let the SEP client pick up the new policy and test it out. Does the problem still occur?
Should you prefer to disable startup scans altogether, you can do this at step 7 by removing the checkmark which reads "Allow startup scans to run when users logon".
Also, check this Article:
Best Practices for Installing Symantec Endpoint Protection on Citrix and Terminal Servers:
http://www.symantec.com/business/support/index?page=content&id=TECH91070
Hope that helps!!