The only thing I've found that may be affecting you is that you can no longer mix an input board with analog and digital inputs. Whereas a Comtrol board you can mix and match all 16 inputs they must be split into groups of 8 that are either digital or analog running on an E2. I haven't started a store conversion yet, only have test boards running at the shop.
Sounds like an excellent place to start checking.
hi my name is norman from ny work in supermakt ref for five yr in the feild for eight yr it come to my attention that yo work on co2 system for ref could yo direct me to infor on them will like to know any infor i could get