Well, there's no 1:1 relationship between the number of files in the ROM path and the number of correct (, ...) or not found sets the audit may find.
If you don't trust QMC2, run "mame -verifyroms" over your ROM path - the information will basically be the same, except that it's textual (QMC2 parses this text).
Anyway, without a concrete / simple example I'm unable to help you. Pick a set which you think should be correct (but is shown as "not found"), then check the corresponding files... also check what the ROMAlyzer has to say about it... and then post your results here.
Oh, and excerpts from the front-end log would help, too:
17:48:10.384: verifying ROM status for all sets
17:49:14.293: checking real status of 2830 sets not mentioned during full audit
17:49:14.508: done (checking real status of 2830 sets not mentioned during full audit)
17:49:14.510: done (verifying ROM status for all sets, elapsed time = 01:04.126)