Okay, I give up. I'm completely stumped on this one. If you know the answer, great. If not, PLEASE ask your trusted friends and coworkers.
The problem is that some parts of some windows of some applications are missing. As an example, in one app, the background of modal popups is gone leaving just the window title bar and the text & graphic of the popup. I say that this element is gone, rather than transparent, as a click on what MUST be part of the window's missing element passes straight through to the app underneath.
I have included a screen grab of an example. The gray horizontal line below the Properties element is actually the bottom edge of the window. The text and 3 squares above the Properties element should be displayed in front of a light gray background, not the green of the bamboo desktop image. Clicking on a visible element of the foreground app acts normally, but clicking between the words "HFS/HFS+" and the Properties element passes through to the desktop. It exhibits this behavior even though the location clicked MUST be part of the application window.
If I had control over which elements behave this way, I would be happy as a clam. This behavior is the Holy Grail for some GUI's, but to my knowledge has never been possible on Mac's without specifically programming multiple windows that move as a group. That isn't what is happening here. These are standard parts of Cocoa windows and views, but they aren't being served by the window manager.
Only my account is having this problem. The behavior is consistent from launch to launch in effected apps, and from boot to boot as to which apps will have a problem.
Platform is a Late 2010 MacBook Air. OS X 10.6.7, 2.13 GHz Intel Core 2 Duo, 4GB Ram and 250 GB SSD. The OS and all software and drivers are up to date as of the post time of this question.
I've got 30+ years of experience slingin' code and getting my tie caught in cooling fans, but this one has me completely stumped. I would offer 10,000 points if it were possible.