This is really weird. I managed to reproduce the problem by booting with the screen off, with the incorrect resolution confirmed by xrandr. Then I rebooted and it was still wrong. I have 1024 * 768 instead of 1600 * 900.
I thought maybe the monitor is somehow causing it by persisting in whatever contortions it has to undertake to deal with the incorrect resolution, so then I tried shutting everything down and turning off power at the wall for a minute or two. Still no improvement.
Incidentally, it must be hardware detection during boot, not starting X, because you have to do that manually with the Ratposion edition, so the display is always on. Well, you could do it blind, but I just turn the display on if it isn't already.
The physical proportions of my screen fit the higher resolution, too - it is almost twice as wide as it is tall.

