Folder(Set)Renames are always fuzzy. If ClrMamePro finds an unknown folder/setname, it will check all files inside this set.

ClrMamePro checks the CRC32 (or SHA1/MD5 for chds) of the found files, matches them with its internal database and uses the setname which got the most checksummatches. This doesn't have to be the correct setname of course but usually it is.

In case of CHDs, you only have one file and so ClrMamePro can't really decide if it should use the clone or the parent, since both sets use that one file.
If you keep the roms unzipped in these folders, too (and not zipped in a rompath), the set+name check should be able to find the correct name.

Roman Scherzer
ClrMamePro