After looking around online for some time trying to come across a solution that worked for me, I stumbled across the post above about using metacity --replace. So, based on that, I was pretty certain that Compiz was the root of my mouse issues. After playing around with Ubuntu Tweak, one of the menu options, "Enable Metacity's compositing feature", mentioned that I had to manually disable visual effects in appearance.
So, after disabling Visual Effects (System>Preferences>Appearance>Visual Effects then select None), the mouse is suddenly working again. I don't know if this will be a permanent solution or if it will start giving me problems again, but I thought I'd mention this solution.
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