Thomas,
I noted in your original post that the album tracks seem to have been ripped using iTunes. You said you were going to rip them again.Could you try this time ripping in FLAC using a different software, like dbPoweramp ? I am wondering if your problem could not originate from the iTunes-style tags,which are very different from the FLAC-style tags I am more familiar with. You could also try to retag your tracks using Mp3Tag, and see if this changes anything.
I know this is a lot of work…