If it's working (which are assured that ir is) then the processes are still working. As you make no note of how you've got things configured, there is no way to try to pinpoint your answer.
If you have this account POPing your other accounts, then many things come into play. Assuming the last commented 15-minute cycle, then approximatrly every 15 minutes or so, your other e-mail account is accessed. Some traffic flows. Now we get into the quantity and size of the e-mails involved. Worst case, only a portion of your e-mail from the other system gets pulled down before the connection is dropped so as to move on to the next account-holder's e-mail actions. Which e-mails get pulled are probably based on how that other server offers them, one could assume that in most cases, it might be the most recent e-mails first.
If you have your other accounts forwarding to this account, then there might be issues due it being down for so long, and the other server has 'handled' the situation somehow. Perhaps simply deciding that the Domain no longer existed and stopped trying to send, perhaps by putting some time-delay on the sending actions before gettng around to trying again, perhaps sitting there with yet another e-mail advising you to 'do something' to clear up the situation.
Just a couple of possible scenarios tossed out, trying to work with no data provided.
I'm sorry, I neglected to detail any fancy setups because there are none, I use webmail directly. Anyway, the messages are finally there this morning so the answer was yes, the backfill was still happening and they were not showing up in chronological order.