I was not sure what you meant by 'checking the vendor's credit account;' what I did was make a new vendor invoice, then go to cash -> payments, and search the screen for any unchecked boxes.
What he meant was: Go to AP -> Vendors -> Search, click the Search button, find the vendor you were talking about; (now the vendor will be shown on the right frame) click on Accounts and - if there's only one account, which I presume is your situation - click Save. That should fix your pre-existing vendor.
Aha! I misinterpreted the word "check" there. I've looked back & it seems all I was doing when I thought the problem was fixed was clicking "post" on a payment screen that was effectively blank because I had clicked the "X" box on the line for the payment. Therefore, there was no complaint.
When I do follow these instructions, when I get to the vendor account page, I see buttons that say "Save changes" and "save new". If I click the latter I get an error ("Conflict with Existing Data. Perhaps you already entered this?"). If I click the former, after a wait from the server I get the same page. But there is still no change in the behavior on the payment page: trying to pay an invoice with the "apply discount" box clicked gives the same "Wrong number of accounts" error.
yrs
matt