Apple Music does not support FLAC, but you knew that already, right? Good. The second most common cause of problems with FLAC files is having outdated software. Before pulling your hair out, check online, get the latest version and try again. If that doesn’t work try another FLAC program. We personally use VLC for playback and the command line flac tools for converting to WAV.
The source of the problem is that a lot of older software can’t handle FLACs with sample sizes greater than 16 bits or sample rates higher than 44.1kHz. We encourage artists to upload the highest quality sources they can get their hands on, and more and more tracks are 24-bit/96kHz. On unsupported software these FLACs sound wrecked by static, or superloud, or they just won’t play at all. Some albums have a mix of 16- and 24-bit audio which explains why you might be able to play some tracks but not others.
The bottom line is that FLAC is great but software support for FLAC is still iffy, especially for the newer high quality formats.