MapKnitter has a limit to how far users can zoom in (+) to do stitching.
Try using the browser zoom function to make things larger when you cannot scale the viewer any larger with the "+" key or button. It will only enlarge things but this may be helpful. Combine this with toggling transparency and outline to improve the overlay process. The MapKnitter toolbar will not render properly but all of the image adjustment shortcut keys will still work.