Wrong channel layout for FLAC 3.1 channels.
The FLAC is made from DTSHDMA source. Conversion was done with ffmpeg 2.7 and eac3to 3.29.
Both ffmpeg and eac3to preserve the source channel layout, and they write the metadata tags for this.
Mediainfo shows this (for the DTSHDMA, ffmpeg FLAC and eac3to FLAC):
Channel(s) : 4 channels Channel positions : Front: L C R, Back: C
This is a 3.1 channel layout.
VLC shows this in codec information: DTSHDMA source: channels 3F1R, ffmpeg FLAC: channels 2F2R, eac3to FLAC: channels 2F2R
So it seems VLC fails to read the channel layout tags correctly.
Please read the channel layout so that VLC can play it back correctly.