AP batches are always out of balance if they have checks written against them (and they are on accrual)
When an entry is first made in AP it creates a batch at that point the batch shows the debit to the expense and a credit to the accounts payable.
When the check is written the batch is updated with the check number and the debit to accounts payable.
The credit entry, which would be to the bank, is on a CD batch and is not shown on the AP batch.
The reason this is, is because you may have a check that is paying invoices posted in several batches. The entry to the bank account is one amount not each of the amounts of the invoice.
I encourage our customers to use the AP Journal reports instead of the batch report because it shows all entries