Order Time allows you to take a payment on a sales order without creating an invoice (aka Ship Doc). When the payment is synced with QuickBooks it creates a negative A/R (i.e. a credit). Then when the ship doc is created, the credit is applied to it appropriately.
This mechanism will be disturbed when QuickBooks auto applies credits as it chooses. Then when the payment is synced back from QuickBooks to Order Time, the payment may be applied to different sales orders!
To keep this from happening, turn off the Automatically Apply Credits setting as shown below.