I don't know when this started happening, but it has been several months since I first noticed it.

Basically, when I go to a preferences menu of some programs, the preferences window is completely hidden, but the program see's it as being open. This prevents me from interacting with the preferences and the actual program. So far I've noticed it on Adobe Illustrator and Netbeans. Illustrator when I select edit - > Preferences -> An Option. On Netbeans it happens when I right click on a site and select properties.

Here's a link to a screen shot after I click on the preferences menu (I don't have enough points to post an image yet): http://www.jestep.com/images/screen-2.jpg. Note that the main workspace is grayed out. I have to hit Escape to close the hidden preferences window.

I've tried unstinstalling, completely wiping the registry of any trace of the program and reinstalling. Thought it may have been a multi-monitor issue when I switched from 2 monitors down to 1, but menu's were not on other monitor when I plugged one back in. I've reset workspaces, windows display, windows performance settings, changed resolution, safe mode, everything I can think of. I cannot figure out what would cause the same problem on completely unrelated software, and I cannot reset it by reinstalling. Any help would be greatly appreciated.