Hi,
There are two tiers, "Selling Manager" which is free, and "Selling Manager Pro" which eBay charges for. You just need the free one, which it sounds like you are already enrolled in if you are getting shipping cost information for most of your sales already.
I am guessing that the information wasnt available yet in the API when you downloaded the sale.
To update information for that sale, if you reset the download duration in the Account Information tab to go back far enough for that sale, click the 'apply duration' button, and redownload your sales, it will update any information that is BLANK on an existing sale.
So if it is filled in with "$0.00" just clear that out (highlight the cell and click the delete key, or right click and select clear contents) and then redownload the sales, it will fill in if it is available now.
Let me know how it goes, or if you have any further trouble.