Tried again today, after the SU11 update, I did the exact same flight, same weather and this time it worked perfectly.
I then left the engines running, boarded new passengers and did another short hop from Stansted to Heathrow and again the ILS worked beautifully.
I need to get my landings better though as both times I think i over-flared and bounced badly, I did read somewhere that the CJ4 needs no flare at all, just throttles off at threshold, might try that.