I've fixed it but it wasn't the tags! I was close to the problem in my second post about levels and clipping the input of the head unit.
After messing around with different FLAC files again, I temporarily disconnected the analog stereo harness from the Keg's RCA output.
When the Keg was playing music but it wasn't being sent to the head unit, I noticed that there was low level noise coming through my tweeters that directly corresponded with BMW data bus commands being sent when buttons were pressed and also when there was hard disk activity in the Keg.
I originally had the Keg wired in as shown below, then changed it to the second configuration:
Looking inside the BMW/Alpine interface, it has a pair of small output transformers near the RCA output. So I guess it has either isolated some sort of ground loop or changed the audio ground so that all the noise is removed.
Because of this noise issue on the bus and BMW head units don't have an easily accessible volume reading, I'm not sure whether the output level has also been reduced, stopping any clipping of the input.
Anyway, I'm glad it's fixed and my music is crystal clear again
On the weekend I'll try to find time to get out my multimeter and scope to see if I can work out what's different about the new grounding arrangement and determine the maximum unclipped signal levels from the different RCA outputs with a 1 kHz 0 dB test tone.