Dear Wendy,
Yes, in your current rules, the gift cards are only used in the "Only gift cards" rule. To add the gift card-shipping (.99 per card) to the shipping costs automatically, you basically have to approaches:
1) Use a custom variable to store the gift card shipping and add it to each shipping rate:
Variable=GiftCards; Value=evaluate_for_categories(Articles, "giftcard-SLUG")
Variable=OtherItems; Value=Articles-GiftCards
Variable=GiftCardShipping; Value=GiftCards*0.99
Comment="Only gift card"; GiftCards==Articles; Shipping=0.99
OtherItems<=1; Shipping=8.24+GiftCardShipping
OtherItems<=2; Shipping=13.15+GiftCardShipping
...
2) Use the ExtraShippingCharge feature to specify an additional shipping cost that will be automatically added to the result of all subsequent rules (of course, only to the matching rule):
Variable=GiftCards; Value=evaluate_for_categories(Articles, "giftcard-SLUG")
Variable=OtherItems; Value=Articles-GiftCards
Comment="Only gift card"; GiftCards==Articles; Shipping=0.99
ExtraShippingCharge=GiftCards*0.99
OtherItems<=1; Shipping=8.24
OtherItems<=2; Shipping=13.15
...
This approach is faster to implement, but harder to read if you look at the rules in a few years, as it is easy to overlook.
Please note that the extra shipping charge must be placed after the gift-card-only case, but before the OtherItems<=1 rule, because the extra charge should not apply to gift-card-only orders, but should be added to all remaining rules.
Best regards,
Reinhold
PS: In the gift-card-only case, do you want to have fixed shipping costs of 0.99, or do you want 0.99 per card? Your current rules are a flat-rate of 0.99, irrespective of the number of gift cards ordered. To charge 0.99 shipping per gift card, you need to adjust your gift-card-only rule to Shipping=0.99*Articles