Any new movement is going to cause some pain. I have been walking and hiking for thousands and thousands of miles over the past few decades yet I can still get sore. If you are transitioning from high carb to low carb, read this. Even if you aren't going all that low carb, this info will still help:
The Blog of Michael R. Eades, M.D. » Tips & tricks for starting (or restarting) low-carb Pt II
Female, 5'3", 49, Starting weight: 163lbs. Current weight: 135 (more or less).
Starting squat: 45lbs. Current squat: 160 x 2