I get confused by the terms "stage right" and "stage left" so let me just say, the 0-degree axis of the "S" microphone should point to the left from the audience's point of view as they face center stage.
If that's what you did, and you still got reversed L/R channels, then it's possible that your "S" microphone signals are getting their polarity flipped on the way to the matrix input. Do you have a meter that you can check your cables with? We can go over which pins should be connected to which.
At least there's no other harm done--just swap L and R outputs, and the result should be exactly what you would have gotten if everything had been correct in the first place.
--best regards
P.S.: Just to be very clear, yes, it certainly does matter which way a figure-8 microphone is facing! Every figure-8 has a front and a back. The back is as sensitive as the front--but if you push a "positive-going" (pressure increasing) wavefront at the front of the microphone, the microphone will put out a positive-going voltage, while if you push the same wavefront at the rear of the microphone, you will get an equal, negative-going voltage instead. In other words, the front and back of the microphone have identical response except w/r/t polarity. And the whole way that the M/S approach works is based on using that behavior of the "S" microphone to discriminate between the sounds arriving from the one side versus the other.