OK for the record, Since Dave Hill decided it was his mission in life to confuse all who thought they understood these things, I decided next time I got one in I would have a play. And pay a little attention to what I was doing.

So today I got an 03 plate Mondeo TDCi in with a P2338 code stored and the description on IDS was "Cylinder 3 upper knock limit attained"

So before changing anything I decided to do a little research.

First thing I did was plug in Multiscan as I know this can code the injector correction factors, When I selected Injector programming it gave me a screen with a list of 4 lines of hex data in 8 blocks of 2.

None of this data matched the numbers on the injectors or the numbers on the sticker on the cam cover. This was the same for Autodiagnos too.
The Multiscan also had a misleading interpretation of Cylinder/Injector relationship

Which read:
Injector1/Cylinder1
Injector2/Cylinder3
Injector3/Cylinder2
Injector4/Cylinder4

The numbers on the cam cover did however match the injectors. The first number was for Inj no1/Cyl no1, to the right of that was Inj2/Cyl3, bottom left was Inj3/Cyl4 and bottom right was Inj4/Cyl2.

Injector1/Cylinder1 Injector2/Cylinder3

Injector3/Cylinder4 Injector4/Cylinder2

The Cylinder Numbers ARE the physical cylinders where no1 is nearest the crankshaft pulley and no4 is nearest the gearbox. The arrangement above is as you read the sticker on the cam cover.

I entered the correction factor for Injector2/Cylinder3 and the code cleared instantly.

So to conclude, when the ECU reports a Cylinder number at fault, It is that Physical Cylinder it is refering to.

Hope this helps clarify the situation, (or not)

Mike