[Prodigal Son]

I have these issues as well with my hip flexors, I don't think it is my stretching as I am rather flexible. I do lots of dynamic/static stretching pre/post workout. Mine actually seem to get better as the workout progresses into the later sets, I have been told it is usually associated with Tensor Fascia lata tear near origin points. I have taken the week off hoping they feel better next week, I'm really at a loss for what is causing the pain, it doesn't sound as severe as your trouble though and only seems to occur largely while doing squats.

I haven't been doing squats for years and never had this problem this is a recent problem.