ford focus 1999 3 button key fob remote not working?

Ive tried switching the ignition 4 times in under 6 seconds, I hear the "bong" noise but the red led light above the clock does not stay lit, it keeps flashing. Ive pressed all the buttons on the remote but i dont hear the "bong" noise again.
Ive removed the 20amp fuse at the back of the fuse box and replaced it. Ive replaced the battery 3 times in the key fob. Ive spent over 3 hours on 3 seperate days trying to repair this fault. I think the problem may lie with the red light.
ANY HELP WOULD BE GRATEFULLY RECIEVED!!!!
Cheers.

Jon Mc
April 2009