I just realized I didn't answer one of your questions. The software that assembles the video from the captured frames is called Cinecap. It is essentially claymation software adapted for use with the Workprinter. It also does pulldowns. It is hard for me to believe that it could misalign the fields.
It also occurred to me that one of the causes of the alignment issue with respect to the syncronization of the film advancement and the image grab, could be a damaged sprocket hole.