mb6606 is right, this is a very correctable condition if you understand the origins of the problem. First, though, is to eliminate some more serious structural issues than just muscle confusion. From that point it is just a matter of better negotiating the tensions of the hips and legs that contribute to the symptom, in this case plgolfers formidable discomfort; for others the symptom might have manifested differently.
plgolfer, I would also like to know if you have pronation in your foot placement. I am sure you have discussed much of this with your PT so let's work with what you know and then make applications of good information specific to your case.
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