If you repay them before their last payroll period in 2004, then they should give you a W-2 that reflects what you actually earned and the withholding on those earnings.
There is an IRS Revenue Ruling out there that involves overpayments/repayments that span tax years. I don't recall the details, but it isn't pretty, involving amended W-2's, amended tax returns, etc. If you don't repay them until 2005 and they follow that Revenue ruling, you might well become good friends with H&R Block. So, try to repay this tax year.
And start reconciling your checking account each month!