I'm guessing you need to enter a different Standard Entry Class for that vendor in Vendor Maintenance. Here's info from the Help files:
Standard Entry Class
Type a class code to identify the type of transactions that will be transmitted for this vendor. If no code is entered in this field, the code entered in the Standard Entry Class field in ACH Maintenance will be used.
When ACH electronic payment files are generated, a separate file will be generated for each bank code/standard entry class code.
Expand/Collapse item Example
Type PPD for a prearranged payment and deposit.
Type CCD for a cash concentration or disbursement.
Type CTX for a corporate trade exchange.
For example, the standard entry class for vendor A and vendor B is PPD. The standard entry class for vendor C is CTX. If you pay all three vendors electronically using bank code D, two ACH electronic payment files are generated. One file is generated for vendors A and B, because they both use the same standard entry class code. A second file is generated for vendor C.
This field is available only if the Enable Electronic Payments check box is selected in Accounts Payable Options.