I'm pretty sure payouts are still being done manually.
Also, if it was done according to the miner list, which lists miners only by the largest worker, not total hashrate, that could explain things, though I don't agree it makes much sense.
I doubt "manual" means actually entering numbers manually lol... more like "manually running a script".
And I would presume it would run by largest balances first, but who knows - could be any given sort order, but based on me receiving a payout, I'm guessing it has something to do with those higher up the chain. Or maybe it was just random. Who knows.
Anyway, PoolWaffle obviously still has the "Note: Payouts are slightly delayed" on the site for a reason - I am sure everything will be cleared up in around 12 hours.