Yes, weird about it being a 65E and throwing an ISS code...

Could it be in the TCM wiring? Ive heard all T42s are wired the same way, but Im pretty sure thats incorrect as 06-07 TBSSs can use the same TCM OS but 08-09s cannot. (They're 70Es, but that shouldnt matter for this argument.)

What year ECM OS are you running? Are they a matched pair (E38/T42 OSs), as in a factory option?

EDIT:
OK, so its throwing the P0717 code but it is a 65E with an ISS? (Or is the ISS part unknown at this stage?) Try changing the ISS table I mentioned a few posts ago (D7026) and killing the DTCs, but you're correct that just disabling the DTCs wont do it. I think the biggest thing is to make sure the ECM and TCM OS are a GM factory matched pair, then go from there (if they aren't already).