2006 RR sport Supercharge wheel Alignment issue

Hi. I have 2006 RR sport SC I recently had clunking noise from front end and I took to my body' s shop and we change the front lower control arms and sway bar links. After that we put the car on the latest Hunter Wheel Alignment machine for 4 wheel alignment after correct the rears technician started adjusting the front but for some reason we can not bring the front wheels to measurement not even close enough to tolerable range. Now steering is off half turn and of course that throws the HDS code since the car travels all time with wheel turned half way with old control arms I was off alignment on the steering may be half inch and same mechanic did alignment on this car before so he knows what he is doing. But missing something. New arms are genuine LR parts complete with ball joints. All tire stock 20 inch and tire pressures are checked. The only thing is front right height sensor is changed before and every since that side is little lower and car is not %100 level would this course that much throw on the alignment machine or simply this is a dealer procedure I don't even think the dealer has same machine my body just got this6 months ago and paid lots of money.
Thanks to everybody