11.10 Mouse Doesn't Click Inside Applications!

Only recently (around a couple of months ago), I installed Ubuntu and I currently use a dual-boot PC that has both Windows 7 and Ubuntu 11.10.

The problem I've been facing is that, when I run Ubuntu 11.10 (whether installed or just off the USB), an awful lot of the time, the mouse works fine but does not click inside applications.

For example, I perfectly able to click on the network settings on the top-right corner, and it works fine.

But if there is anything that opens up a new window, the mouse is not functional in that window.

So, I can click on the Firefox icon for example, and it would load. However, any clicking in the new window that pops up would not do anything. I can't click on the Google search text box, so I'd have to keep hitting 'Tab' to get there, and then type. The keyboard works fine.

It's the same with anything really, not just Firefox. If I click on My Files, the window pops up, but I can't click on any icon in there. It just doesn't react.

Apparently a few others have also had my problem. These are the cases I've found after searching:
http://ubuntuforums.org/showthread.php?t=1801465
http://ubuntuforums.org/showthread.php?t=1596081
http://ubuntuforums.org/showthread.php?t=1863100

Allow me to point out that very, very rarely, the exact opposite happens. Say I am in Firefox, I can ONLY click inside Firefox. Any click outside of its window will be disregarded. In fact, I can't even click 'x' to close it.

Unfortunately I haven't stumbled upon a solution to this problem after searching, so I'm curious to know why this happens to just a few of us, and how I might be able to fix this issue.

Thanks in advance!