UPDATE: To reset the preferences go to the maya/20xx-xx folder in your user/documents folder and in the prefs folder just delete the file userprefs.mel. This will leave your hotkeys, shelves, scripts and addons intact.

If you delete the entire prefs folder you will wipe your shelves, hotkeys, marking menus, and some scripts. All that seems to get corrupted is the userprefs.mel file so this is all that normally must be deleted.

What I do is create a copy of that file (A KNOWN GOOD ONE!) and then create and run this script that I now keep on my desktop since it's something I need to do several times a day (thank you autodesk may I have another!).

file: fixprefs_2012.bat (I have one for 2013 as well since it is also borked!)

========== batch file to fix maya prefs ===============

@echo off
cd c:\users\ctbram\documents\maya\2012-x64\prefs
del userprefs.mel
copy "userPrefs - Copy.mel" userPrefs.mel
echo fixed Maya 2012 userPrefs.mel

pause

=========== end batch file =============

For major catastrophies I also keep a copy of the entire maya folder so I can just replace the entire folder if things get really screwed up. I recreate this copy whenver I add scripts or addons. This way if you have to completely wipe the maya folder you are not left with all your plugins, scripts, hotkeys, marking menus, and shelves ganked!

This is a fecking SERIOUS bugs and autodesk just simply ignores it and for the cost of maya it's TOTALLY unacceptable and I don't care if it affects a small number of cuxtomers the cause needs to be identified and fixed! I use dozens of applications as complex or more complex as Maya without any issues!

Maya has two problems one with managing memory and one with writing and reading data to and from disk! I have proved this with debug dumps when autosave crashes and when delete history crashes. In both cases I can show windows is either trying to access disk (reading or writing) or is trying to manage memory (alloc/dealloc). I have even sent the god damn dumps to autodesk and all I get back is the sound of crickets chirping!