Sorry for the delay.
After re-investigating the issue, I found out that the file can be played in Liquidsoap, with some problem.
The 24 bits FLAC sound is too quiet compared to 16 bits FLAC, I don't know what cause this, but I can hear it as usual via various players (foorbar2000, windows media player, mplayer, etc)
The issue of track begin skipped was caused by the "eat_blank" operator which I instruct it to skip a track which is too quiet.
BTW, The actual root cause of this issue is that the decoding of 24 bits FLAC file is too quiet.