Nuke your prefs to kingdom come! :) You might consider doing this, just make sure you backup any scripts, shelves, etc. you want to keep. You could just rename the existing prefs folder and start Maya. Then copy from the old one.
Do you see any warning or error messages in the script window when this happens? I've noticed that the context menus sometimes don't use long (unique) object names for querying nodeType, so the command to build the menu will fail (in Maya 2008 anyway). You might see a warning saying something like "more than one object…