Is the car seat itself uncomfortable? Is it padded or hard? If you think it may be the car seat itself, you can experiment by putting her in the seat in the house and seeing if she just doesn't like it, or doesn't like being confined. She may be bored--staring at the back seat all the time, which was part of my son's problem--he did better when I finally thought (duh!) to give him some toys.
She may just be a sociable little girl and likes company--I think that's what my son's problem was. He did okay when I was in the back seat with him, but since I couldn't sit with him and drive, we had some horrid trips. I was afraid to put my older son (19 months older) right next to him when he was so young, but you could try to put your son (since he is so much older) right next to your daughter and see if he can keep her company.
My son finally stopped when he got older--I was more conscious to give him toys, he had his older brother right next to him, and he also got turned around. He actually did better facing backwards than forwards when I first changed him, because he could still see my older son easily.