Our web site isn't equipped to implement all upgrades because we are treating upgrades for this product differently. You just may have to contact sales directly to get the discount.
Our upgrade center will only look at individual purchases for individual upgrades, since that was what we always did before. It doesn't consider when you have purchased multiple things that were combined, since this is the first extension we have released that does this.
Our upgrade policy is to give an upgrade for any purchase you have made of products that are now in the combined extension. You get 100% of the money you spent up to 50% off.
Then we get even more generous if you have spent more than the price of the new extensions on the tools that are integrated into the extension, which it sounds like you have, then you can get the upgrade for just $39.99. You'll just have to call our sales line and get Lauren to process special discounts for these cases.
The upgrade policy is described on the product FAQ page: faq.php