You don't need to nuke the registry stuff.(posted 9027 days ago)When you start MAME32 after changing versions, it'll ask you if you want to use the old config data (whether or not it's an older version). Choose 'no'.
This'll take care of version-sensitive data. (I have five different versions of MAME32... 37b6, 37b8, 37b9, 37b11, and 37b13k... and I know this does this.)