My guess, and this is only a guess, is that the threshold for the DTMF digits the NEC hears may be pretty tight, and the Fax machines may be a little too sloppy in their DTMF generation.
If you put a DTMF decoder between the system and a pots line you may see what the NEC is not recognizing.
I'm not familiar with the IPK II but you may want to look into where the touch tone receivers are, and think about replacing that piece of hardware.