Probably the chassis batteries were so low that most of the DC current from the house batteries were going that direction rather than the starter. Also your battery charger might not have enough power to have much of an effect after an hour considering the size of the engine start batteries needed for a diesel engine.
Holding the AUX START for a minute or so pushed a lot of amps into the chassis batteries to give it a bit more of a charge than what your charger could provide. Started dead cars many times by connecting the jumper cables and just let it sit for a couple of minutes.