The battery *should* be what's causing playback issues with FLAC.
I don't know what Raptor is though. Try a different encoder. Also, make sure the tags are Vorbis Comments, as if for some reason it doesn't use the proper tagging, that could potentially cause problems.
Our FLAC codec itself isn't known to have any issues at this time, so it's *most* likely your encoder creating some sort of not entirely standard files, that our codec is less tolerant of than whatever else you use to play them. This doesn't mean there's not a problem with ours, it's just less likely, since you really are the first report of this problem I've seen.
As for build stability, other than the random freezing that seems to affect all 4G builds until that bug is resolved, there isn't any known to be particularly better or worse for FLAC playback.