Jeannette10 --
You answered your own question. The IRS was clearly subtracting the amount you owed in April from the $1200. The small difference could be a small computational disagreement or an interest / penalty charge regarding the April payment you made.
Why don't you cool your jets until the deposit hits your account this coming Friday. It's possible that you'll still get the full $1,200 if their computer updates its figures to reflect your recent payment.
If not, the $1,200 refund is actually an advance on a $1,200 credit you'll be entitled to on next year's 1040. If you don't get the full rebate this year, you should get credit for the difference on next year's return. Or, the IRS may send you a tax refund check in the next few weeks since you've now "overpaid" your taxes.