That explains why I saw a -0.005 balance on my account, did a manual payment this morning and now I owe $0.60 to the pool

At my current speed, it would roughtly take ~3 hours to get back to zero balance.
Luckily the duration of this double awarding was not very long (~8 hours). As a result, even the most harshly affected (payout requested JUST before it was caught) shouldn't require more than half a day to rebuild their balance.