I restarted my computer with 12.04 and on boot-up it took a long time to boot into the system after logging in.

Then the settings even though still set correctly are not being read properly. Left handed mouse and capslock as ctrl are still selected but the os doesn't recognize them. Even if changing from right handed to left handed it isn't picked up.

Also the video settings seemed to be forgotten and will only allow mirror mode. The font and default icons got changed as well.

Compiz settings and shortcuts are working and operate correctly.
Anyone had this issue or know where to look for a fix or what could be going on?