I'm curious, has she been evaluated by a pediatrician or chiropracter for scoliosis?
this is great advice! assuming you are doing everything right, and especially if there is any bruising on the spine from the carseat, this is likely the cause.
those here who know me from the old babycenter board know that this is why Damian was (though he wasn't voicing it as extremely) first never happy with his back comfort in a carseat and always had bruising on it from about age 2 and then, went on to not be able to remain upright in a booster when falling asleep even at age 6 (to the extent his head would be in his LAP)
I not only put him back in a more padded harnessed seat (the Regent), which cured the discomfort, had padding which prevented the bruising, but also had a harness, which kept him in a perfect posture position... and I also tried to ensure he didn't slouch or do things that would worsen the problem at home, but this was the crucial period where, after a car ride, you'd see an increase in bruising and/or he would seem to have more of a curve going on. In addition, he was examined by his pediatrician and referred to an orthopedist who confirmed the scoliosis I suspected for some time and the pediatrician had not been able to see for the past two years. (To help the ped be able to notice it during the Adam's test (where they check the spine as the child touches his toes with straight legs), I had taken an extra 30 minutes of driving with him in his booster first... he was 6 and past 40lbs, so otherwise fine to use one.
Anyway... the orthopedist said while they can't officially recommend it, as it is expensive and not every scoliosis is severe enough to warrent prescription seats, that harnessing is definitely the way to go to prevent it and to keep it minimal or keep the spine straight so the child can outgrow one that has been caused by poor positioning of the spine.
Sure enough, when he outgrew the seat, he didn't have the problem in the booster anymore and has since seen his scoliosis decrease and now have it gone.
But before we assume that.... do check the following
1. take the carseat and pull the cover up... feel it to be sure there is nothing caught under the cover or in the cover and be sure that the part of the seat along his back is smooth.
2. when you install it, make sure that there is no twisting in the seatbelt or latch (assuming he is forward facing, this could cause the problem) strap.
3. when you place him in the seat, NO bulky clothes, coats, etc. Be sure he sits all the way back and sits up good and straight. If he is rearfacing, the straps come from at or below the shoulders and if forward facing, at or above.
4. Make sure the straps are nice and straight and tighten them until you can no longer pinch any slack in them at his collar bone (after pulling all the slack up into the shoulders, unless he's in an evenflo triumph... then you would check at his hips and pull slack down into the lap straps and tightening the straps). Position the chest clip at armpit height.
I do suspect it could be positioning, as you referred to a curve in the infant seat. Infant seats are straight... just as any other seat... the only bend or curve is where the child's bottom goes (seat crack in the seat crack).
He really canNOT use a booster at all as he is far too young and far too little to be mature enough to sit in one and/or have the seatbelt fit him properly.
But assuming all that is already done, then here is another, though a little scarier, possibility for the pain, since you describe it as being far more severe than a typical scoliosis would be.
He could have a tethered cord... as explaining what that is and the symptoms would make this even longer, I'm providing a great link.
http://neurosurgery4kids.net/tetheredspinalcord.htm#signs