The payment tolerance warning appears when you post an application with a balance within the allowed tolerance. You can then choose how you want to post and document the balance.
Open the 
General Ledger
Setup window.
On the Application tab in the Payment Tolerance Warning field, insert a check mark to activate the warning. To deactivate the warning, remove the check mark.
In the Pmt. Disc. Tolerance Warning field, insert a check mark to activate the warning. To deactivate the warning, remove the check mark.
If you select Apply to Oldest, you should deactivate the payment tolerance warning. If it is activated, the program, will ignore the warning.
If you choose not to display warnings, you must make sure you have specified the account to which the payment discount date tolerance and payment tolerance are to be posted in the G/L Setup.
The default option for the Payment Tolerance Warning window is Leave the Balance as Remaining Amount and for the Payment Discount Tolerance Warning window the default option is Do Not Accept the Late Payment Discount.
Blocking Payment Tolerance for Customer or Vendor
Payment Tolerance and Payment Discount Tolerance