There is the main window of the app. Then there are compose/reply windows. And there's the Pros window - more particularly the Updates section.
1) I have the main window with a compose window on top of it. I then switch to another space, and when I get back to the Usenapp space, the Compose window is now underneath the Main window. This is a bit annoying if some time elapsed in switching back and forth. I'll wonder what happened and assume I submitted the post. Then two days later I find the unsubmitted post again.
2) I have the main window with the Prefs window on top of it. I go to the Updates section and click on Check for Updates. Now, this works OK if there are no updates (the message is on top, therefore visible), but IME if there is and update then nothing appears to happen as the Download Now window is underneath everything. Is this still the case?