My money is on a firmware problem. My Rev C has a split right shift and to make it work right (with the shift on the inside and the FN key on the outside) I had to swap K3C & K3D in QMK. I don't know anything about the programming tool you're using but I'll bet the problem is something similar. In fact I'll bet your non-functioning "right shift" key is really a FN key, if you can think of a way to test it.