When you pay a regular invoice with a credit invoice, Accounts Payable prints a check for the difference as long as the difference is for a positive amount. Accounts Payable does not print a check if the difference would result in a negative check.

Occasionally, the full amount of the positive invoice prints on the check and the credit invoice does not print at all even though you selected both for payment. Some reasons this can occur are listed below as follows:

• The Vendor has One invoice per payment checked
• One of the invoices has a joint payee
• The check printing order in Accounts Payable settings is set to Job and there are different jobs on the credit invoice and regular invoice
• The Bank account use method is set to System automatically assigns per distribution in Accounts Payable settings and the invoices have different banks assigned to them
• The credit invoice has retainage
• The selected invoices have different Payment types assigned
• The vendor for these invoices is type Summary and the name is spelled differently between the positive and credit invoices

• The One invoice per payment (or One invoice per check prior to version 9.8) box is selected for the vendor:
  1. From the Setup menu, select Vendors.
  2. Enter the appropriate vendor ID.
  3. Click the Payment Settings tab.
  4. Verify the One invoice per payment (or One invoice per check prior to version 9.8) box is cleared.
  5. Click Save and then click Close.
• One of the invoices has a joint payee:
  1. From the Tasks menu, select Select Invoices for Payment, On-screen List.
  2. Click Start.
  3. Select one of the invoices that you wanted to pay, and then click Detail on.
  4. Scroll all the way to the right and verify whether the Joint Check box is clear or not. If this should not be a joint check and there is something entered in Joint Check, clear the field.
  5. Click Move to List, and then click Detail off.
  6. Repeat the previous steps and verify each of the other invoices you wanted to pay. If the invoices have a different Joint Check payee entered, separate checks will print for each payee. Any invoices with a Joint Check payee print separately from invoices without a Joint Check payee.
• The check printing order in Accounts Payable settings is set to Job and there are different jobs on the credit invoice and regular invoice:
  1. From the File menu, select Company Settings, AP Settings.
  2. Click Orders.
  3. In the Payments section, verify whether Job is selected. If you print a separate check for each job, then you cannot pay your credit invoice and regular invoice together if they have different jobs.
  4. To verify the job on the invoices:
     1. From the Tasks menu, select Select Invoices for Payment, On-screen list.
     2. Click Start.
     3. Select one of the invoices that you wanted to pay, and then click Distributions.
     4. Note the Job column and what jobs are assigned to the distributions.
     5. Click Invoices to return back to the list of invoices.
     6. Repeat the previous steps to determine if the jobs are different on any of the other invoices that you want to pay.
• The Bank account use method is set to System automatically assigns per distribution in Accounts Payable settings and the invoices have different banks assigned to them:
  1. From the File menu, select Company Settings, AP Settings.
  2. Click Payment Settings (or Check Settings prior to version 9.8).
  3. Verify whether the Bank account use method is set to System automatically assigns per distribution.
  4. Click OK twice.
  5. From the Tasks menu, select Select Invoices for Payment, On-screen List.
  6. Click Start.
  7. Select one of the invoices that you wanted to pay, and then click Detail on.
  8. Note the bank account listed in the Bank Account box. Click Move to List, and then click Detail off.
  9. Repeat the previous step and verify the bank account for each of the other invoices you want to pay. You must assign the same bank account to both your credit invoice and your regular invoice if you want to pay them on the same check.
• The credit invoice has retainage:
  1. From the Tasks menu, select Select Invoices for Payment, On-screen List.
  2. Select Retainage invoices only box.
  3. Select both the positive and credit invoice with retainage to release and pay retainage.
• The selected invoices have different Payment types assigned. Refer to How do I change the payment type on an AP Invoice? to make the Payment type the same on the selected invoices.
• The vendor for these invoices is type ONETIME or Summary and the name is spelled differently between the positive and credit invoices. Refer to How can I view the payee name and address on an invoice for a summary vendor in AP? to view the payee name. To change the payee name, refer to How can I change the payee name or address on a summary vendor invoice?

If none of the above solutions resolve the issue, try to pay the invoices with a Quick Check instead of through Print Checks to see if there's a specific error message generated.