First of all, "working" and auditing sets are 2 different things.
Auditing might result in a 100% correct set (i.e. all files are there and correctly named etc) while the game is still not working since MAME does not emulate it correctly (yet). It's pretty common that a set requires more than its own set files. Depending on its merge mode it might require files from the parent set, a bios set and device sets. So if you want to play game xyz you might also require belonding bios, device and parent sets as well.
Secondly....I don't know where the idea comes from that you need a full rebuild first....So...use the scanner and run it with all check/fix options enabled. It tells you what is missing...and THEN you can use the rebuilder (or simply drag'n drop files in the scanner) to ADD them.
The rebuilder destination should point to your rompaths (where the correct names are added to), while the source (if not using drag'n drop) points to a messy folder with all kind of unsorted stuff.
You're done when the scanner results tree does not show any entries.
What do you mean with "but their drivers are not in the clrmamepro system/software scan list." ?