I don’t really know why they dont show up.. But I know flac can (needs?) be transcoded on-the-fly by firefly.
When a song is requested, firefly transcodes the stream to output as something like WAV or PCM.
This puts the decoding load on the server instead of the client. (which usually has more power)
However, I doubt this transcoding has anything to do with showing up in firefly..
Is .flac in the music files extensions? (See adminpage->configuration->music files->extensions)
Also, note that linux is case sensitive, so a .FLAC file is probably not recognized.