I’m one of the ones that was looking at it earlier, and was able to fix one of the footnotes just by messing with one of the lists a bit below it, changing the length of it enough to change the page layout. The other two weren’t fixed when that happened, but I bet if I had been trying to I probably could have done something that would have.
My guess is that you’ve probably hit some kind of case, like a rounding error, where something is right on the edge of being incorrect, and a little tip one way or the other rights it. Deleting a good chunk of text like the ToC would definitely change the scenery, as would the paper size.
You could probably make a similar impact by slightly changing the amount of padding around chapter breaks, or little tweaks to the margins, anything that would disrupt the page wrapping, even just a little bit.
By the way, the reason I messed with the list in the first place is that I spotted it was being hit by this bug. Note the flash at the top of that thread, which links to a workaround.