Check on the following first:
- The user trying to create the File Upload has access to the Bank Link object in Positive Pay
- The user trying to create the File Upload is doing so at the root level in Intacct
- Or at the entity level of the Intacct bank account defined in the bank link. The bank link will not be shown if the bank account in Intacct was created in a different entity from the current one the user is in.