Well, whatever is causing the problem, "Program 1" is not it. In fact, for an Instrument Track, it's automatic, defaults to Program 1. If you are not dealing with an instrument set to change programs, it would tend to be quite irrelevant.
I have never used Program 1 or the like in Cubase or Nuendo, nor have I ever used the Instrument Track (always Rack, ie., F11 instruments).
But I tested it, and here Synchron Player responds to automation in the automation lane as assigned, from an Instrument Track with SP instantiated.
link to screen movie: auto. in SyPlayer working
(Dim. A, CC20 is crossfading vibrato types and Mix 1 Volume is automated there)