To add: I just noticed that changing the font size has an effect. It's strange. It seems like longer books tend to be more likely to be stuck further down the screen, to the point where with the longest ones you can just make out the top sliver of 'parchment'. If you decrease the font below 100%, the lower you go the higher long books will open on the screen, until eventually at 70 *most* will open in the middle of the screen. The opposite applies. Turn up the font and longer books will be invisible, hidden below the screen, and shorter books that used to appear in the middle will open lower down.
I'd originally wondered if somehow my gedosato downsampling was doing it (even though it worked fine before), but no. Even without it the problem exists.