OK, so Firefox was running extremely slow, I ran it in safe mode and still slow, so I rebooted and when she came back on, I wasn't at the regular Unity login, it was like a classic Windows login (where I had to enter my username and password manually, not a list of users). I logged in and only my desktop was visible (with icons and my wallpaper). Nothing else. I was able to open a terminal with Ctrl+ Alt+T and typed...

sudo unity

...which got it up (albeit with the default icons on the launcher ex. I had unlocked Libre Office and it was back). In "Startup Applications..." there was absolutely nothing at all...

This happens every time I reboot. Thunderbird de-synced from my Gmail but Pidgin is still connected. When I do Ctrl+Alt+L it locks the screen as normal, but I have no option to switch user. I have the only account on this computer but I cannot access the main login screen to get to my Guest account. I'm not very Ubuntu-savy, but it's pretty clear that I'm starting in some sort of safemode.

I am on a fresh install of Ubuntu 12.04.1 LTS (just installed it last night).