A brief summary of the information I've found so far on the "black windows bug" from around the web:
Someone having similar difficulties with KDE4 on Linux:
http://www.nvnews.net/vbulletin/showthread.php?t=118778 (This links to a KDE bug tracker entry where the KDE devs blame nVidia and there's no real useful information as far as I can tell, but you may wish to check it out.)
Some proposed fixes for Compiz, which I've not tried, but plan to mess around with later:
http://forum.compiz-fusion.org/showthread.php?t=1762
A fix for it (which stinks, since one ought to be able to enjoy their video card):
System Settings -> Desktop -> Desktop Effects: Un-click the checkbox for "Enable desktop effects"
Note: This doesn't fix the first bug I mention - may need to submit it to the KDE bug tracker and see what they say there, but getting a screencap of it doesn't seem possible, which makes life a bit harder...