If it's messing on the bottom side of fabric, the problem is usually on the top. Is your thread in the takeup lever where it belongs? Mine has popped out after thread breakage and it's usually the last place I look. I've been known to tape up the opening on the takeup lever. Some Pfaffs simply don't like one brand of thread. Depending on the wrap, some spools need to be upright, and others horizontal.
Did you check the tension on the bobbin? Hold it by the thread and if the bobbin slides down the thread, there is no tension on the bobbin. You did put the bobbin in right way to? I've reversed it by mistake.
What happens if you take some stitches by just turning the flywheel? If it messes up then, the problem is probably on the thread/mechanical end as you bypassed the motor and electronics.
Is the foot all the way down? Sometimes the presser foot lever sticks.