Yes - changing to ceramic pads on a vehicle originally equipped with semi-mettalic pads (from the factory) will likely cause a problem if the factory rotors are still present.
Ford found this out themselves when they made the change to ceramic pads in 12/03. Between then and 8/04, they continued to use the same rotors as before. Because of premature rotor warping issues caused by the new ceramic pads, they are covering warped rotors on Expeditions between these production dates (TSB). I doubt, however, that they are paying for new pads when the rotors are replaced.
I helped a friend change out the fronts on his '04 XLT (bad rotor shudder @ 26K miles). At the time, we didn't know about the TSB. We put ceramics on and new rotors. No problem since. However, when he found out about the TSB and took the old rotors in to his Ford stealership, they wouldn't do anything for him.
Bad Ford Expedition Engineering: Brake pads, oil dipstick location, and oil filter location. They should make their engineers work in the garage for 6-months.