> formats/file extensions check fine with GoodSNES and used to fail in my ClrMame

You need headerless romfiles for clrmamepro. Goodtools ignore headers, ClrMamePro doesn't.

> unmodified. What a mess! Hopefully one day ClrMame will be able to fix all
> these things in the future.

It has nothing to do with ClrMamePro. You simply have to remove the headers from the mentioned files.