Any Carbon app has the same issues. However, our use of windows is more extensive than most other apps, and our apps are some of the most widely-used on the platform, so it's much most readily apparent in our apps.
As I mentioned earlier in this thread, we've shown our code to Apple and asked for suggestions for how to fix it. We've implemented their suggestions in our code, and they've also made changes in dot-releases of Leopard, which have improved but not completely fixed the problem. If you'd like to know more of the nitty-gritty details about this particular issue, including the extensive work that we've done with Apple to try to resolve this, check out this blog post from one of our senior developers:
risks and rewards. (It's a long post; the stuff that's specific to Spaces comes down about halfway in. Look for the paragraph that starts with "Bear with me while I shift gears now".)
Since you seem to be quite knowledgeable about how software should interact with OS X, I'll assume that you have some professional experience developing Mac software. In that case, we're always looking for great developers to join our team. Feel free to PM me with your resume -- the pay's great, the benefits are awesome, and you get to work on Mac software that's used by lots upon lots of people.
Regards,
Nadyne.