I wouldn't think it was a skimming scheme, but a mistake.
I used to work in a bank a zillion years ago, and while I'm sure things are done differently now, the basics should be about the same.
Example: The IRS deposits Dawn's check for $37.00 and the IRS shows $37.00 in their account. It clears Dawn's account for $57.00. There is no actual cash that changes hands, just paper. But the numbers between the banks are off by $20.00. The $20.00 is then placed in a holding account until the problem is figured out why (since so many checks clear in a day it's hard to pinpoint the exact problem right away)
It used to be my job at the bank to find those problems sitting in the holding account and reconcile them.
It should be an easy fix.