For what its worth, I too have come across this exact problem.
I built the 1359 install using rsimmons documentation on my LS11.
Funny that – I followed the procedure described in those instructions too 😉
And oddly enough FLAC no longer seems to be working on my setup (I’m sure it used to, and I haven’t changed anything!)
I only have one album encoded in FLAC, so I hadn’t got around to investigating the problem. Could well be the same issue – I’ll give it a go.