From time to time, a payment may not be properly created during the synchronization in QuickBooks. A record of the payment may show in QuickBooks, but the internal keys linking the payment to Acctivate may not exist. The next synchronization may properly create the payment in QuickBooks or Acctivate, but this will cause multiple payments to now show.
The solution is to simply delete both payments out of QuickBooks and run another synchronization. (Note: You must be in Single User mode to fully delete the payments from the QuickBooks side) The synchronization should now properly create the correct payment in QuickBooks.
There are some variations to the scenario. For instance, the second synchronization may also create a duplicate payment in Acctivate as well. Again, the solution to delete both payments out of QuickBooks should remove the duplicate, errant payment from both Acctivate and QuickBooks.
If you continue to have problems with a duplicate payment, contact Acctivate Support by submitting a Support Request here.