I've already submitted this to the bug tracker(mistakingly saying the problem also effected keyboard input, btw), but I wanted to see if anybody else has this problem. Whenever I use an app object(like a button, list box, etc..) and click on it, mouse clicks will no longer register. Keyboard input still works fine, but the mouse won't register any clicks at all. Here's an example .CAP:
Broken Mouse Input
By the way, this was just recently, because this problem didn't happen with previous versions.