Mess' romoutput is a mess ;) It has a lot fake clones (set x is 100% set y) and some other bad entries. But that shouldn't effect clrmamepro in the described way. I will check it later today. If I remember correctly you shouldn't keep mess sets full merged, because it has some wrong entries which will overwrite each other...well..I will do tests later.

Roman Scherzer
ClrMamePro