I just tried out the new motioncor2 wrapper and realized that there is an error in the script.
The electron dose (FmDose) is set to the total dose by the wrapper. In fact it should be divided by the no. of frames, since the framedose is asked.
Maybe you can fix this in the next release, for now it only helps to change the dose during import of the movies to the framedose. All settings in the extra command string are overwritten in my case.