You all have great textbook, kinesiological arguments above. I appreciate the feedback. Here's an update on experiences in the gym over the past couple weeks.
I have the book Starting Strength which I refer to quite a bit regarding squat technique. The problem is, I was using a lot of coach Rips cues such has "hips back" and "limiting forward knee travel"while still using a high bar position. As a result, and my coach observed this today, I have not been letting my knees travel far enough forward during OH squats and high bar back squats. This may or may not be why the increased hip flexor soreness.
Any how, I concluded when doing high bar back squats, OH squats, or Front Squats, I need to sit my butt straight down and let knees travel further forward.
On the other hand I have also played around with the low bar back squat position in recently. the lower bar position does significantly change the dynamic of the lift and Rip's coaching cue such as "hips back" and "limit forward knee travel", and "hip drive" do work well with the low bar position.
My conclusion is I can't mix up the coaching cues on the two lifts or I am going to stress my hip flexors.