Are you using Spaces? I lose windows occasionally too, especially when I Apple+Tab a lot, but it's 'cause I have Spaces activated. I think the windows are gone, but they're not, they just moved to one of the other desktop spaces... strange. So, I save my Window Layouts so I can reset... curious if anyone else has this happen to them w/ Spaces activated??
"The deepest blues are black" - Foo Fighters
(this doesn't help me when I'm chroma keying!)
Please delete the preferences of Apple Motion. This usually fixes the problem.
Go to the following location: your home folder/library/preferences, then find the file called com.apple.motion.plist and delete it. (while you are doing this make sure that your motion is not running).
Restart you Motion, you should be able to see all.
If not you have to reinstall Apple Motion from original disk.