Sorry about that. I blamed Dungeon Tactics because it's the latest addition to my mod set and I've never had problems with them before. It's possible I just got really unlucky and my three 'likely' end cities weren't there.
Ah, I didn't check those items. In fact, I think I checked every item but those. Thanks for the help!
EDIT: Yep, I finally found one. Seems 'likely' End cities are less likely than advertised.