Or are you turning off transcoding for FLAC, and thus allowing the pure, raw FLAC file to stream for at least some of your user's Players?
This is what I'm doing ...and yes, I'm doing everything you've advised already and tried all the external players.
I've settled on XBMC as my preferred external player, because it can talk directly to Subsonic and can be remote controlled with an IOS device.
Alternatively I also like to stream from the Subsonic server to the IOS device using iSub. I'll try streaming some high-res flac's again with XBMC. My "users" are just myself, my wife and daughter.
Even if I manage to get XBMC running on a mac to stream the high-res stuff satisfactorily, iSub would not be able to support them, for sure, hence the need for a down sampled duplicate of these files.