When you modded that Sync 3 unit, the SYNC itself senses the speed in which the vehicle is traveling. So if the speed side thinks you are attempting to work a menu function - the speed threshold to operate a menu function tells the system to stop and notify you of the condition. So it tends to think you're endangering yourself trying to do something that can be considered distracted driving.
That is what SYNC thinks, it doesn't mean that it is.
Did you try using the passenger seat-belt and clicking it in place? It may then stop annoying you because it thinks someone else is tuning or using SYNC so it will let them do it, Might need to put a 2-liter bottle or some weight on that seat cushion so the system can see "occupancy" and trigger this mode so you can fiddle with SYNC.
See if the occupancy trick works...