I've never used Auctiva's checkout...long before I was a seller, there were always problems with combined shipping whenever I had to check out as a buyer using Auctiva. I myself find it much easier to manage my sales through Ebay, only because I'm used to doing it that way.
As for the comment in the original post here, I have seen sellers that will enclose something like this in their auction listings to make their buyers feel more at ease:
"Please checkout through Auctiva...it will take you to Paypal where you can pay as you normally would" Or some similar sentence.