For the sake of accuracy, and having given it more careful thought inspired by a good hard nudge in the ribs in w2 Help chat, I should revise my earlier.
My main account was running when the daily bonus arrived and continued running until maintenance took it down. So it might make sense that the daily bonus triggered while the old resources were still active and stayed with the old, even if I didn't collect the bonus until after relogging this morning. Accounts that had crystals were logged out when the daily bonus would have arrived, stayed logged out through maint and were only activated (triggering the bonus window for the first time) after the update changeover to crystals.
Happy investigating!