Have you re-programmed the remote? The instructions are in your owners manual.

If not then I'd be concerned that the transponder in the key is on its way out. If you go down to one working key then you'll need to get the car into Ford to have another key programmed (approx £100) - if you've still got the vague use of 2 keys then you can buy any blue-chip remote fob second hand, get a keyblade cut at any key cutter and program the new key yourself - hopefully before this one dies.