Sounds odd, but I would see if you can get your pelvic alignment checked. If you have a discrepancy between your Left vs Right Sacroiliac Joints and one side is rotated compared to the other, it will change the length-tension relationship (especially with muscles like the Rec Fem and Hamstring). If your Rec Fem is having a hard time firing I would almost wonder if you had a slight posterior tilt which would put it  a bit on stretch and not allow it to fire as well. Easy way to build up angry adhesions/trigger points. I also believe this would cause some issues with deeper squatting. Mike Rice could probably explain it ten times better, no doubt.