Version:            (using KDE 4.3.1)
Compiler:          gcc (SUSE Linux) 4.3.2 [gcc-4_3-branch revision 141291] 
OS:                Linux
Installed from:    SuSE RPMs

I've been having an issue for a while where System tray "Notifications" and Transfer statuses would not appear at all. Apparently, they were spawning underneath the Plasma desktop window. 

This happens under Compiz 0.8.2 in KDE 4.3.1 and 4.3.0 (OpenSuSE 11.1).

Steps to Reproduce this state:

STEP ONE
Start Compiz.
Remove your System Tray Applet from your Plasma Panel.*
Add the System Tray Applet to the Plasma Panel again.*
*This fixes the issue for the time being. It does reoccur naturally, although these steps are the quickest way I know of to reproduce this issue.*

STEP TWO
Start a File Transfer or other event that kicks off a notification message. You may let it hide.
Make the notification visible by clicking on the icon.

STEP THREE
Switch from Compiz to KWin using fusion-icon, other utility, or manually.
Switch back to Compiz.

The Notification should be underneath the Plasma Desktop. Making your "Cube" transparent should allow you to see them.