Thanks for the bug report. I haven't had any problems with books not opening at the last page read, so it may be hard for me to debug this problem, but I'll take a look at it. As far as automatic rotation goes, I have seen that problem, too, but in my case it works for a while, and then becomes unresponsive later. Now that I know it happens to others, too, I'll look into seeing why it happens.
I don't have any problem zooming with any of the various ways to do it, but I don't have a touchscreen, so I can't test that method. Can you explain how you are trying to zoom? It's true that zooming moves the panel off-center in the screen, and I should probably fix that.
It's true that panel detection works best when they have black borders. Most important is that they are separated by "white" space that extends out to the edges of the page. If there is no empty space between the panels, the algorithm will not work. So, it's only good for some books; for others it will not be much use.