First of all...use 3.30 since it's the current version and its scanner is much faster.
2nd of all...I guess you didn't understand the rebuilder completely. The rebuilder rebuilds anything it finds. If a rom in the source is shared by 500 different sets, the rebuilder will create all 500 sets with that one rom in it. Of course this doesn't mean these sets are complete. The rebuilder doesn't know anything about set-completeness and it's not its purpose. En contraire...it's the main feature.

So if you don't want to get the other files created, you have to disable the sets you don't want. Settings->Sets has several options to select/deselect games.

Roman Scherzer
ClrMamePro