Please explain it more. How did you send in the payments? Did you send them in with a 1040V voucher? If you used a 1040ES slip that was for an estimated payment for NEXT year so it didn't get applied to the tax due.
Or the IRS could have adjusted your return and you owe 2,000 more.
And your post doesn't make sense. You are mixing up Direct Deposit for refunds and payments for tax due. And a voided check means it was stopped and cancelled. What did you receive? You receive a Refund. Did you have a 3300 Refund or a tax due? How could you cash $1,100? Did the IRS send you $1,100?