I was probably in the same boat as you. However it was more that it was just an entire different movement and position. The weight at least is I would say at least 10% less than my low bar squat.
If your training for oly lifts though, I would say this really doesn't matter as much since the squat is mainly an assistance to your main lifts. As for both squats and especially the Front Squat the more you do them the more your body will become accustomed to the movements.
Make sure your doing your mobility work where it's needed. Greg's book has a whole section on the flexibility standards for the lifts and mobility work.