I was having an issue with notifications in Plasma "not appearing", and didn't notice until I flipped the cube in Compiz that the notifications were spawning underneath of the desktop window:
Normal Desktop...

When Rotating Cube (cube is transparent, so you can see through it)


I've never reported any bugs in KDE, so if I need to do so point me somewhere and I'll go ahead and file one with as much detail to reproduce as I can.

This is Present in 4.3.0 and 4.3.1 with Compiz 0.8.2 on OpenSuSE 11.1.
If you need a test case, I'll see what I can dig up. Removing the System Tray applet and re-adding it to the main panel seems to stay the problem for a short time.

Edit:
When switching to KWin, the popups show on top again. Switching back to Compiz brings them back underneath the Plasma desktop window.

Yes this seems to be a problem of Compiz - I'm not sure the Plasma devs can do anything about it. Nevertheless, it's worth to let them know about the issue. You can file bug reports at http://bugs.kde.org (registration needed). Please do a search first to see if it's been reported before.

Thanks for taking your time, don't forget to post a link to the bug here. :)

I submitted the bug, along with steps to reproduce the problem. Can anyone confirm these steps work on their installations?

You may see the bug report at the following URL.
https://bugs.kde.org/show_bug.cgi?id=207506