After running some updates this weekend to my desktop, I found that upon rebooting, I no longer had a desktop to log back into. After finding out that Compiz was crashing with a segfault and no more info, I had to use the Gnome Fallback mode until I had time to look further into it.
Today, I created a new user account and imported my home folder into it (thereby re-creating the problem). After a while, I drilled it down to the .config folder, but no matter what I did to permissions or removing folders within it, it simply didn't work. So if you suffer from the problem, take a backup of your .config and delete the old one. Log back in and gradually move your configs back. Eventually you'll get to the bottom of it.
I can't find a way to reproduce the problem, so filing a bug has also be difficult :(