good deal,
yes i supposed if everything checked out ok then there is always that possibility that the controller itself may not be seeing the signal in that circuit for some internal reason.
controllers arent cheap though so hope that is actually what it is.

tblsht diagram says to check stop lamp output wire #788 (pin7) at vsm connector, if resistance is less than 0.5 ohms then repair short to ground in harness circuit, if no then replace the vsm.