Fake rectangle/window visible under some windows tricky question here.

I don't know how long this has been going on, but I noticed it only recently. My semi-transparent windows have a “fake” square/window beneath them, which is visible (it also project a shadow, but only when the window is in foreground.  

Screenshot:
 (the textedit window serves just as a white backdrop).

Video showing behaviour:
http://cl.ly/132M2T0p3j0E210d0S2K

I initially thought this was just TextMate, but I noticed this on terminal.app too (semi-transparent too).

I am running 10.6.6, have no “strange” hacks or input managers installed AFAIR.
I understand that this is probably a very exotic bug, so tools that can help me track down the cause are welcome, and I'll gladly accept such an answer.

Thanks in advance,

A.
I've seen a similar effect before, awhile ago. It's probably a program running in the background that has a transparent window on the desktop. Do you have anything running in the background that uses transparent windows or window overlays? I seem to remember an old version on Norton AV doing strange things like this many years ago.