This problem has been going on since I got 10.7, and is persisting or even getting worse since I updated to Mavricks. The best way to describe it is thru an example-

Let's say I'm working in Safari. Everything is working fine. Then, I'll switch to another app by clicking on it's window, for example, I'll click on Messages to shoot back a reply. When I click back to Safari, keyboard and mouse inputs don't work! The only way I can regain control of the app (Safari) is by clicking on the apps top bar, which then causes the app to jump left or right. If I'm in Messages and I switch back to Safari by clicking said top bar, it works fine. Same with switching back and forth using command-tab.

I've narrowed the problem down to this - the first app (Safari, in this example) is, for some reason, deciding that I'm in the process of dragging the window around.

This could be just an oddly persistent glitch in my system, but has anyone else seen this before? Perhaps a misplaced default write... somewhere along the line?

Update
A PRAM reset did absolutely nothing