Upon further reflection I think what I said above was wrong. The difference between manual-mark and auto-mark *should* be just that with auto-marking you don't need to explicitly mark before you can settle. I'm guessing here as I haven't found any good docs from Verisign on this but it seems logical. Therefore, my problems with settling must have been something else; I'm guessing that query wasn't returning what was expected.
I will look into this in more detail when I build a payment module for Verisign's PayFlow, which I'll be doing after Bart and I finish defining the payment contract.