If the cert is less than the base fare, the system finds you the first fare higher than the cert. You must call in and have web support (not reservations) ticket it for you manually at the lower fare (so always search for pricing without the cert first). Confirm the balance to be paid before giving them your cc (should be tax/fee only)
They have gotten better a processing these, but maybe it was just an easy Rez the last couple of times.