It all started with a message offering a Partial Update.
I know what you're thinking. "Oh joy. Another new user who isn't smart enough to know better than to hit the Partial Upgrade button."
I'm pretty sure I did it the "right" way, by first going into Synaptic, and checking to see what was going to be removed. To the best of my knowledge, nothing important(Just a telepathy lib called farsight, and a couple other IM-related things, which I don't use.) I don't know if I was supposed to do this, but I unmarked most of the removal-marked items, and the only one removed I think was Empathy app, which I don't use.
A restart later, and on the surface everything seemed fine. There was just one issue, where the Unity bar wouldn't hide. The Update Manager still had updates(A lot, actually), but it wasn't offering a Partial Upgrade, so I installed the updates.
Another restart later, and the Unity-bar problem was fixed. However, It looks like I can only run in Ubuntu 2D mode now. All the panel transparency stuff, etc, doesn't work, though that's just graphical related. The main problem is the fact that the Unity Panel is no longer displaying the system menu.(See image)
I suspect that Ubuntu isn't getting along with my GFX card anymore, and it thinks it can't run Unity3D.
One more thing, Apport did detect a graphical-related crash, and a bug report was automatically filed. Should I wait for the bugfix?