Because we had this issue with last year's changes to the B&B.com program and we stopped accepting them, I added this policy to the list that has to be checked when guests book online:
GIFT CERTIFICATES: Please note that gift certificates of ANY type cannot be redeemed by booking online. To redeem a gift certificate you must phone the Inn at (123) 456-7890. Guests making a reservation using the online booking system will be UNABLE to use any type of gift certificate towards their invoice total.
So they have to phone to book and I at least know they are using a GC and I ask for the number. Otherwise, if they book online and use a credit card, they don't get to use the certificates when they arrive.
Edited to add: You can do what others here have suggested and just take the cards, and use them yourself for your next get-a-way...you don't eat any commission that way, just don't get the $$ now.