sometimes mine'll squeak for the first minute or so of driving (all kinds of speed bumps on my out of the parking deck) then they quiet down... usually happens if I haven't driven the car for a day or so. Haven't a bunch of people complained that the stock Focus brakes are kinda shitty, are yours stock? Or, I don't know if this matters, but maybe if the rotors are dirty they cause noise?? I hate squeaky brakes, make the car sound awfully ghetto!
Do you drive on gravel? Out here in the boonies, one trip on gravel, you get dust in there (oh yeah, stock brakes) and they'll squeak until you use 'em about four times. Then it's all hunky dory! Until you hit gravel that is. [mad]