Hi,
From your description, some possibilities come to mind....
Combined Shipping discount rules and "Promotional" shipping discounts rules are actually two different eBay settings. They actually display (check-off) as separate in the one-page lister for Calculated Shipping. Promotional rules will override the normal combined rules, when applicable. Here's the eBay explanation on Promotional:
http://pages.ebay.com/help/pay...ional_shipping_rules
Also, whenever you change those settings at eBay, it's necessary to sync those settings to Auctiva in your Auctiva "ebay Settings" under the Account tab (note the warning on one-page just under where you check-off for applying the rules as reminder). That's most often the cause of the combined or promotional rules failing to get correct result. However, I've seen that fail on more than one occassion for whatever bug is currently the cause.
Another possible cause is failing to create an "Add Rule" on a single listing, i.e. combined rules are for multiple listings ONLY and the "add rule" is for multiple quantity purchased from a single listing. Add rules are done on the one-page lister for each individual listing. You indicated it was two lots of the same item, so that possibly is probably the more likely cause. Usually, add is automatic for weight(s), but not for S&H.
Your description suggests the 2nd was shipped free using calculated weight, so that does have me slightly puzzled for exact cause. Do you have a lising number(s), as the shipping details might give me a clue?
Danno