I've experimented with different tagging options in CDEX including no tags, and tried some tag editors on the results, but no FLAC files that come out of CDEX seem to work on my iHP-140. That includes files made with tags turned off and then Vorbis tags added.
Then I ran the 'file' command on some files that work and some that don't. There is a marked difference. Here's one that works:
10 - The Black Angel's Death Song.flac: FLAC audio bitstream data, 16 bit, stereo, 44.1 kHz, 8460144 samples
and here is one that doesn't:
10-The Black Angel's Death Song.flac: FLAC audio bitstream data, 16 bit, stereo, 44.1 kHz, length unknown
(both versions play in Audacious)
so in my case it seems something else is wrong. Whether this helps the original poster is another matter.