I have had similar but more complex problems through several versions of Ubuntu. Some left mouse functions don't work, while others are fine, and there are other symptoms. Right now, I can't use the Application menu on the toolbar. Now I can. Now I can't again.
I just played a game of Mines. Everything works, except the final mouse click to start a new game or quit. (Workaround: tab between buttons, and use Return to activate one.)
I most often get the problem in Firefox, where I spend most of my time writing (at FLOSS Manuals and various blogs) and researching.
Previously, I could escape this problem temporarily by creating a new user and moving all my files over. Not this time in Meerkat. Or maybe there is a way. In my experiment, I reused an old account name. What if I use a completely new name? I have to restart now, but I'll let you know.