Matt,
I think the second option is more reasonable, after all, there is no good reason for a media file to be marked as a system file, is there? It is indeed very important to warn the user about this, a simple message like "ignoring file x for reason y" would suffice IMHO.
Sincerely I was starting to think there was a bug in the code...
Also, while googling about the issue, I think I saw someone complaining that the software was importing a bunch of flac files while ignoring others for no apparent reason. It´s likely the some problem, don´t you agree?
Well... thanks for your quick reply and accept my congratulations for the awesome product!
Warm regards,
Fábio.