I bought a spare key from eBay, it works as a remote but I can't match it with the IMMO using Vag Com. As I can match other keys, I assume that the keys transponder is wrong and needs replacing.

I've come across this site Hickley Valtone :: Keys and Remotes - Transponders that sells transponders but was unsure which one was right for a 55 plate Fabia VRS. Anyone know which one will work?

Out of that choice the AKTP2 looks to be the closest, having never purchased one I can't comment on whether it will work.