Well, I figured it out if anyone's curious. The PDF file I was trying to use was a totally valid (and efficient) PDF, but since the whole 1000-page volume was compressed together as one unit, the JBIG2 symbol table at the start was quite large. Probably the Kindle doesn't have enough memory set aside for that, which is why it didn't display.
I compressed the file again, but this time compressing each page separately and stitching them all together at the end. The file is slightly larger, but now it displays fine on the Kindle (and pretty fast too).