Hello,
I see 3 issues here -
1) Over deployed Licenses.
2) Communication issues between clients and SEPM server.
3) Pop-up from Symantec Email Proxy
1) In reference to the Licenses, could you let us know for how many Licenses are you carrying on the SEPM?
Since there were 250 clients already reporting to the SEPM, I assume you were carrying 250 licenses on the SEPM and you haven't added the extra 50 licenses, correct?
Incase, you are already carrying enough Licenses, then check this Article:
Symantec Endpoint Protection Manager is showing over deployment of clients
http://www.symantec.com/docs/TECH168121
2) In reference to the Communication, check these articles
Symantec Endpoint Protection Manager 12.1 Communication Troubleshooting\
http://www.symantec.com/docs/TECH160964
Troubleshooting communication problems between the management server and the client
http://www.symantec.com/docs/HOWTO55017
3) In reference to the Pop-up from Symantec Email Proxy, Here's a link to the official corresponding Symantec article: Many Unexpected Pop-Ups from Symantec Email Proxy are Displayed
Hope that helps!!