I didn't ask whether the vendor has a balance, I asked whether the TRANSACTION has a balance. From the Vendor List, double-click on the vendor, then click on the Transactions tab and look at the "Current Amt" column.
If the transaction has a balance, and the vendor balance is zero, there ought to be another transaction with an offsetting balance, and these can be applied against each other, as long as they are not checks. Let us know.