I can comfurm that everytime my setting get messed up all I do if delete the "prefs" folder under the "maya" folder in "my Documents" aswell as the maya.env (This one time thats was what was wrong) As soon as you restart maya they get replaced with new ones and its just like opening maya up for the first time. It also the file that I backup the most and just recopy over if something else goes wrong save time setting everything up agan.

good luck