Are you absolutely certain you recorded in ms?
I would setup the recorder and do a test to see if I could reproduce it recording in ms and xy.
The only time I have lopsided results is when the mics are slightly out of alignment. That’s using 2 separate mics though. That shouldn’t be a problem for you. One thing you could try is offsetting the side a few samples at a time to see if you can get the image centered when summed.
Edit: just saw you recorded in a different format than thought. 