This is a weird one.
Out of curiosity I had clicked on the Guest Session option at login, to see what it was like. Now, when I log into my original user, all of my desktop customizations are gone and I'm presented with the default desktop! What happened?! Restarted lightdm and then the machine, which didn't get the job done. I have another user on the machine whose settings have not been affected.
I'm not sure exactly where the problem lies, so I'll try to give a few examples: My international keyboards are gone, as is ibus Chinese input. My settings for the trackpad (i.e. two finger scrolling, two finger right-click) are gone. My wallpaper image is gone and it's back to the unity default purply thing (even though on the lock screen, it is still there) The apps docked to the launcher are back to defaults.
I tried to take a peek at my hidden files in the home folder, and looked at the only one I had edited by hand, .gtk-bookmarks, and my personalizations are gone! As I write that, I now fear that ubuntu has erased/replaced my settings files, though I hope it hasn't been destructive and that this information may be stored somewhere. I could go back and start changing everything by hand again, but this is weird and needs a mention! Any thoughts? Running 12.04. Thanks!