Mark has some very good ideas regarding menus, however, rather than delete the *.mnu files I recommend copying and/or moving them to a safe place (along with your MNS files) so that you may replace them in the event of something screwey going on....
Incedently I just recently migrated my AutoCAD from one computer to another and the new system had a fresh install of AutoCAD....I was able to retain all of my setting by following the following simple rules:
Place all custom programs,menus, and other files in a common location AWAY from the default AutoCAD programs.
Before migrating, export your profile to a new ARG file.
Open the registry with Regedit and export the key:
HKCU/Software/AutoDesk to a registry file (*.reg)
Move your custom files, ARG and *.reg file to the new system.
Before starting AutoCAD, place all of the custom files in the same location in reference to root folder of AutoCAD (presuming you are migrating to the same version just from one system to another)
Merge the registry file
Create a new shortcut referencing the arg profile as the current one.
Start AutoCAD with the new shortcut.
Everything will be EXACTLY like you had on the other computer.