Y96 is a valid low altitude airway according to the navigraph desktop charts app and the aircraft FMS allowed me to enter it in the Flightplan (as it's using the navigraph data).
Its interesting that deleting Y96 fixed the issue though. Maybe the issue is with the navigraph data ??
Anyway, I'm having a great time with the CL650 - its awesome. I don't think I've ever seen such a level of system simulation and attention to detail.