Rain: I don't know if you'll see this post several months after yours...but if you do, this may be due to one of two things
a) A limitation of the software that you're trying to run in multiple desktops. The software may lock itself so it can only call one instance so e.g. you can't overwrite something in one session with what you're doing in another.
b) You may be running mDesktop in non-administrator mode and trying to run the program in single-user mode (or vice versa). Apps will open on all desktops if they have a higher priority/access level than mDesktop.
As to the virus warnings: for a while I used McAfee (or was it Symantec?) - in any case, it identified a file, legitimately part of windowsXP as being malware. The reason: because it could be used by a virus to hide a window, because the windows program allowed
you as an end-user to run it to hide windows. In other words, the virus scanner thought something was malware using a "guilt-by-association" heuristic, which is utterly ridiculous. As I understand how mDesktop works, it hides and displays windows depending
on which desktop you have active. It may use this core Windows file to do so or it's own method that may have very similar code (I don't know...I haven't looked in detail at the source code), either one of which may be tripping HitMan's heuristics. I've
been using mDesktop for a couple months now, and love it, despite having several bugs input to the system. I haven't had any system problems on this system since I installed it, so if it's malware, it sure does a poor job doing malicious things;)
This is my first post on answers.microsoft.com, but I've had this hotmail account since 1996:P