Josh,
Check these spots to see if Prepayment has been accidently applied:
1. Prepayment Tab - Prepayment % >0%
2. Sales Line - Column called Prepmt. Line Amount Excl. Tax >0.00
3. Navigate to Prepayment/Invoices, off the Sales Order. Here you can see if someone did post the Prepayment Invoice and you are awaiting payment. If this did occur, accidently, you can perform a Prepayment Credit Memo to reverse. Then remove the prepayment % on the Tab and Sales Lines.
Hope this helps.
Thanks,
Steve