It sounds as if it works as usual when you go back to the 661. When using the 661 as original it sounds as if the only connector is the 16 pin and the 14 pin is not used. Is that correct? If only the 16 pin connector is used then the PWM must be coming from the usual control pins 3 & 4.

This leads me again to believe that the adapter harness is not wired correctly or the Deere controller is not setup properly. Does the Deere need some type of implement switch or a jumper? That would be required with some Ag Leader situations.  Some type of Master switch must be involved somewhere.