Check the configuration in IMG Financial Accounting -> Bank Accounting -> Business Transactions -> Payment Transactions -> Electronic Bank Statement -> Make Global Settings for Electronic Bank Statement. Check the Posting Rules out there.
Settings in the above transaction are per chart of accounts. Are all you company codes using same operational chart of accounts? Have you checked the above electronic bank statement settings for the chart of accounts assigned to the company code where you have this problem? In the same transaction, please also check the Assign External Transaction Type to Posting Rules sub-dialog. I can't think of any other place to check.
Moreover, you said incoming payment in your question - it is ordinarily supposed to be posted to customer, which is happening in your case. Why do you want to post it to vendor?
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