Although I've been using CLRMAME for some time now it seems that I've run into a simple(?) newbie question:

First: I updated my roms using the rebuilder and the split roms setting, which seemed to run fine.

However, some clones contain identical roms which the parent set also has. The clrmame docs explain that the rebuilder has to work on a file level so this may be expected (??).

However, I would like to use clrmame to remove these un-needed romfiles and I would expect the scanner to do this. Sadly, this doesn't happen as the scanner states that all files are OK.

Is there a way to create "real" split sets with clrmame of my current collection?

An example: two of the files in question is are:

mkla1.zip and mkla2.zip

both files contain the mkg-u106.rom file which I wouldn't expect to be in both sets.

Can someone please explain to me if the sets are wrong, and if so, how to have clrmame fix them?

thanks!