Apple programs not responding to mouse clicks

Several Apple programs have stopped responding to mouse clicks. If I switch out of them to another program or the Finder, the mouse works as expected. They do respond to keyboard commands, so they aren't frozen or locked up and nonresponsive because of that. They just don't respond to any mouse clicks, but do respond to keyboard presses (like cmd-tab, and the usual key combos like cmd-O, cmd-Q, etc.)

These programs have stopped responding to mouse clicks: Preview, Textedit, Messages, Contacts, Remote Desktop, Calendar, App Store, Calculator, Game Center, Pages, iMovie, Font Book, iBooks, Notes, Mail, Garageband, iPhoto.

Works: Compressor, DVD Player, Final Cut Pro, Keynote, iTunes, Numbers, Pages, Motion, Safari, Image Capture, iBooks Author, everything in the Utilities folder.

I have yet to find a non Apple program that shows these symptoms.

I don't have this problem when logged into another account on the same computer. The problem persists when I boot into Safe Mode.

I've tried deleting preferences files, and any files/folders I find in the ~Library/Cache folder, followed by a reboot with no success.

Anyone have a fix, or am I going to have to wipe and restore?