Is your machine in a sewing cabinet so the machine bed is flush with the table surface or are you using the extension base that comes with the Bernina? If the latter I would suspect the extension table is causing drag on the quilt. My machine is in a recessed cabinet but I have had this happen while piecing when I hit an area of bulk and the quilt did not feed through nice and evenly because the pressure foot got hung up on the bulk.
If you can't resolve the issue, it sounds like you will have to go back to quilting on your vintage machine.