Since the patch didn't change anything other than in the continuous viewing mode, I believe the problem is very likely not related to this patch. Maybe I'll try to use the original ipdf binary to see if the problem exists there.
As for the margin problem, actually if there is not enough space, it's probably a margin and should be skipped. Current threshold is 1/3 of the screen to detect this. If its not skipped, the display is not aligned to the edge of the page, but instead it follows previous display area.
Indeed my first solution was to align to the edge, but then I often found myself losing track of the text I was reading because the new content doesn't start from screen top. Ideally one should clip out old content (or gray them) and center new content that is displayed. But I didn't see a quick way to do the clipping. (maybe I'll figure it out if trying harder :-)