I was messing around with CompizConfig Settings Manager recently and I'm not really sure what I did to cause this issue, but now all new windows are opened at 0, 0. This means the title bar is positioned beneath the menu bar in the window z-order, making it very difficult to grab and move the window.
Here's a screenie that may explain it a little better:
I was pretty much just experimenting in CompizConfig Settings Manager, I reversed any changes I made (to my knowledge), but I may have overlooked something. How can I fix this?