I had a user complain about screen flicker while trying to use tools on a server via remote desktop. The server in question was 32 bit windows 2003 running citrix presentation server 4.5. This was not wide spread so only the one server was having issues.
Searching the Net I found a technote at Microsoft which seem to address this issue.
I downloaded the hotfix, installed it and rebooted the server and the problem was solved.