I'm certain I didn't flag 'em myself - but I still feel like a right fool for not checking the most blatently obvious option.

Oddly, in the original album playlist, Disc 1 was flagged 'ignore as child' but Disc 2 was not. When I copied the Disc 1 and Disc 2 playlists to the new temp album playlist, Disc 2 become flagged as well. This seems to agree with your theory, especially as before doing this, I'd cleared out a number of albums/playlists I rarely listen to.

If it helps, it was with Version 36 of Jemplode.