I've experienced the same problem with Spaces. Sometimes I completely lose my archicad file just because I went to check my email in another space (Kinda annoying). This is never a good thing when your in a Teamwork project and you can't find you way back to it from another Space. It almost seems like it disappears in Apple's Spaces while the program stays active in the background somewhere.
I have had some success using the F8 command with spaces rather than my own shortcuts to toggle in between them. Thus I can have AC10, AC11, AC12, and email in there own space. Also when Spaces gets confused and pulls half your application into another space, you can always select the top part of the menu bar (your current app) and drag it back to the space its supposed to be in.
I don't know if this helps you any...but this has been my experience with Spaces.