Itís been a couple of years since Iíve installed one of those little Reliance or GenTran type panels, so I'm going from memory here, but as I recall, the ungrounded side of those AFCI and GFCI cbís are completely out of the loop once you flip those switches and transfer over to generator power, effectively removing their protection from the circuit, although the circuit neutrals remain connected to the cbís.
Iím not sure how this lack of protection plays into the NEC, but it sounds like it could be another touchy issue to deal with.
I believe the cb tripping occurred the instant line power was restored, so I guess a momentary imbalance could indeed be the issue with that. Once utility power is restored and the cbís reset, they would function normally again.
Itís good you had the option to use the interlock. A lot of times the HO provides the transfer panel they picked up at the big box store, so not always an option.