There are two possibilities. One is that you are big (in length) for her. She can contol things better in other positions than she can in that position. In that position she can't control the depth of your penetration and the speed at which you thrust and it hurts. This is less likely.
The...
Let the car warm up before you start driving. Do this by using the gas to keep the RPMs above 1000. It isn't your battery and it isn't your starter. It is something to do with your engine and its baseline RPMs. It should be a cheap problem to fix.