@dudleydes - Have you tried the AdvMAME forums. It might be a long shot but it can't hurt to see if anyone has some suggestions. It sounds like AdvMAME is not doing some cleanup upon exit possibly? AdvMAME Support Forums
I recently bumped up to 3.5 and find it does has some issues that 1.4 doesn't have. I keep both loaded until 3.5 does some "optimizations".