However, they were going to take it all back in one fell swoop from my next paycheck. That would have been a $1000 chunk, which wouldn't have left me with enough money to make a car payment, let alone the rest of my bills. After talking to them, they said they will take it out the same way it came in: take the 3/15 payment out of the 4/15 check, and the 3/31 payment out of the 4/30 check.
I guess I should have noticed this earlier, but 3/15 was my first paycheck, so I didn't have a benchmark to go against. After that, I got an electronic paycheck, and I didn't look at the paystub online, just at the net amount deposited into my bank account. You bet your sweet ass I'll be looking from now on.