Figured it out: as I suspected up there, Whispersync was treating the books I had re-converted to get rid of the [PDOC] tag as completely different books from the ones I had not. Once I removed those old books from my Kindle Keyboard and replaced them with the new conversions, they're all syncing to furthest-page-read just fine.
(My question still stands, though...is this the best I can expect, or should it be remembering my current place and syncing that as well? I'm fine either way, I just want to be satisfied that I have this working as well as can be expected, especially because even furthest-page-read was an unexpected treat.
)