Hi Jason,
As you have already discovered, the primary issue is that the Apache server does not have IPv6 support.
It's ironic that the client is actually capible of requesting policies via IPv6 (Because it uses WinHTTP, a Microsoft library that support IPv6), but the server is not capibile of serving the policies via IPv6. You can verify this by running "Netstat -anop tcpv6"
I have found one work around, that is in no way 'supported', is to use some sort of IPv6 to IPv4 translator.
I'm sure these products are becoming more and more common, for my testing, I used a simple web proxy that is able to listen on the IPv6 stack. Then I told the proxy to forward all web requests to Apache's IPv4 port.
So a quick diagram would look like this:
SEP Client --> IPv6 Web Proxy --> IPv4 SEPM Server
What's nice about this setup is you don't have to 'tweek' configuration files. All you need is:
1) Install a Web Proxy that has IPv6 cabability, you can find these for free on the internet.
2) Configure the Web Proxy to forward traffic to SEPM.
3) Update SEPMs "Mangement Server List" policy to have the IPv6 address of the Web Proxy. (I recommend keeping the IPv4 address as a P2/P3 for backup)
I have tested this, but not extensively. Other than the fact that the Troubleshooting --> Connection Status panel on the client not working when using IPv6, and some strange error in the Sylink.log file, there seemed to be no functional issue. Policies etc did download and apply.
So I can't guarentee it will work seemlessly, but I think it's worth a try. You can even install the IPv6 web proxy on the same server as SEPM.