Ford Focus: Reprogrammed new Remote Key - now won't start.

Apologies if this is repeated info for everyone - I've done a few searches with various bits here and there regarding remotes and locking but I think my problem is a bit more specific.
I bought a Ford Focus 1.8 2000 Zetec, which came with a Remote Key and a spare (blue) key. The remote key would not work remotely but could start the car ok.
After changing the battery on the remote and giving the unit a bit of a clean I decided a new remote was required, so after a few searches here and there I purchased a new remote key, connected the key section of my faulty remote to the new remote, reprogrammed it (4 turns of the ignition, then pressing the unlock button on the remote at the bong signal) which worked to the extent that I can now open the car remotely.
However one unseen side effect is that the remote key will now not start the car. My spare blue key will, so my assumption from this is that the signal from my remote key is not recognised by the immobiliser.
This is concerning because I a) have to use the remote to open, then remember to use the blue key to start the car and b) I now cannot create new replacement keys as I need two keys to reprogram. Weird thing is that I haven't come across anyone with this issue - I've obviously done something wrong!
Any advice gratefully appreciated.
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Swap the glass transponders between the remote sections. The one in your old remote is recognised by the car, but the new one won't be.
Or else use the key part on its own but hold the remote parts close to the lock and program the car to accept the new key. Then you'll have three transponders which the car will recognise, which could be handy if you loose a key. For example I've a blank uncut key which I've programmed to my Focus that way. I'll get it actually cut if I ever need it. You'll have to be quick though!
If you have a Google there's tonnes of instructions as to how to add keys to the car.
Gary.
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Thanks. I know how to add keys, but as said I only have one effective key, and I can't reprogram any other keys unless I start with the two. Unless I've misread your email and you mean something else?
Al
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Ted Danson's evil monkey wrote:

I think what Gary is saying is that you need the non-working part of the original remote that contains the immobiliser transponder. That would effectively give you the two working keys you need in order to match your new one.
If you don't have that any more, proceed to your friendly dealer with your wallet open!
Chris
--
Remove prejudice to reply.

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Ah. That makes sense. There was this voice in my head that told me not to throw it away ;-)
Ta.
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Yes, that's what I meant! I was in a bit of a hurry when I replied earlier! He already has two working "keys"
G.
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Okay, I tried swapping the transponders which didn't work. Suprising as I thought it would do.
Eventually I resorted to taking the circuit board out of my faulty remote and replacing it with the circuit board from the working remote. This must obviously have been the faulty component as that worked.
Thanks for your help anyway guys. I now know a lot more about Fords and remotes than I did last week!
Cheers
Al
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