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i had the same problem, i emailed them and received this reply: Thank you for your message.
If you have received a valid payment receipt from a Sallie Mae payment (email confirmation), but the payment is not showing up in the Common App Online, please use the Other Fee Waiver option or Mail Check to indicate payment. This will allow you to continue with the submission process. Your record will be updated within the next 24-48 hours to indicate the successful credit card payment.
The Support Team