I trace the problem in the align-equal-compile script, where it outputs for most of the utterances:
EqualAlign: the randomly constructed paths lengths: 135,135,135,135,135,135,135,135,135,135
EqualAlign: utterance has too few frames 79 to align.
AlignEqual: did not align utterence
EqualAlign: the randomly constructed paths lengths: 405,405,405,405,405,405,405,405,405,405
EqualAlign: utterance has too few frames 325 to align.
AlignEqual: did not align utterence
It seems weird that it sees 325 frames as too few. Maybe the fst paths are bad? I trained a bigram phone model (I split the data into phones for getting phone error rate)