Sorry for the delay in replying, I've been doing some experimentation to see if I can reproduce the problem. At the moment I have been unable to
I think that I need to stress that this is not a general problem and very few users have ever suffered from it. It seems to be caused by the pop up windows messing up VRPCs DirectX buffer space. Hence my suggestion about contacting the developer(s) concerned to ask them if there is a way of preventing these popups. Your message seems to indicate that you have not (so far) done this and I really think that it might be worth trying.
VirtualRPC has no control over these popups, it doesn't know what they are (in fact it doesn't know they even exist). I've said before that some popups (temperate, Anti-Virus etc) could be very important.
Anyway, lets see if we can do anything about the problem.
If the machine is running Vista then try updating the graphics card drivers and ensure that the drivers are
Direct X V10 compatable (some aren't).
You could try adding the line
AllwaysOnTop = 1
to the GUI section of the Va.Cfg file. I don't know if this will have any effect. This was a flag that was being worked on some years ago, for VirtualA5000, and may not even be present - but it's worth a try.
If you are running Vista then I suspect that the problem could be fixed by an update to XP.