Are you sure it's even related to TrueTransparency? Does the problem problem occur only with that one full-screen application? Which one?

Another possibility: [FAQ] Some windows appearing on all desktops

Hey,

I'm using an application called truetransparency to re-style the exit/minimize buttons in windows 7. To make a long story short, 64 bit applications end up getting copied to any desktop I move to if the application is in full screen mode. Of course it's very annoying, and I could disable the styling but I'm using it to make things easier on myself so I'd rather not. So, now to my actual question, is it possible to prevent applications from moving desktops except through the view all desktops manager?

Thanks, and I really love the program.