Ubuntu :: Unable To Use Mouse Or Switch Windows In Unity Or Gnome?

I recently installed Ubuntu desktop, since I had been running my server as Ubuntu Server on a guest OS on Windows 7 and never really used the Windows part of the computer. Since then, I've been unable to use the mouse in a graphical environment for longer than a few minutes without it starting to act crazy. The mouse moves around normally, but won't respond to clicks (left, middle, or right) but the keyboard shortcuts still work. I'm not sure if things have changed since I last used Gnome though, but Alt+Tab is not working for me either when this happens. Sometimes, the active window is even behind another window, and isn't pulled to the foreground.

After a bit of frustrated clicking and jamming of buttons on the keyboard, sometimes the mouse kind of starts working because I'll notice a right click menu open. But, I am still unable to move windows or click on them to bring them to the foreground, and my mouse presses only work on the current window. And then, eventually, after about a minute or so, it'll stop respond again too.

I saw in one thread that someone had dead spaces where he couldn't click, so he installed and ran Gnome and that fixed it, but I tried using Ubuntu Classic and it is still giving me the same behavior. I'm actually posting this message now in links, because I can't use Firefox or Chrome well enough when it's hidden behind other windows.