To eliminate the error, enter the rounded amount in box 1. In your example, change the amount in box 1 to $1,001.00. Entering the rounded amount is acceptable and will not cause any problems. It's going to get rounded on the tax return anyway. The IRS does not bother with cents.
I'll report the problem, but it's a minor issue so I don't know when they'll fix it, or if they'll fix it at all.
