I've had problems where when I connected to a winXP machine with remote access the new connection would shutdown programs running on the machine. Specifically ICQ, so if it can happen to that, I'm sure there are other programs that can be affected.
The one thing I can recommend to you is install Remote Administrator (
www.radmin.com) and use that for remote access. It doesnt shut down any programs and allows multiple users to be remotely connected and using the same desktop.
May solve the problem you are having.