I've had this happen a few times, when the price of the voucher wasn't exactly equal to the cost of the hire. The difference is usually in the 1 dollar ball park and every time the return agent has just wiped the difference off.
I suspect it arises becauses of currency variations and some agents know that a pre-pay voucher is supposed to be exactly that and handle it correctly and some don't.
The biggest problem with Avis is the refuelling charges. Always check your receipt before leaving the car.