If you use the Prepare Electronic Payments function, the bank account selected defaults to the first bank account in your chart of accounts. This is not the account that we use for electronic payment...
I neglected to say that the system appears to let me change the bank account from the drop down menu, but as soon as I click on "Bank File" to create the ABA file, the system then reverts to the default bank account. I know this because the default bank account/top of the list bank account is a dummy bank account with no bank details listed, so when I try to create the ABA file, I get the message that bank details are incomplete, at that point I can see that it is trying to pay from the wrong account.