Thanks, tried it again this morning and when I got to work as well... the horn is honking when I press any key on the original key in the ignition then nothing happens when I press the buttons on the other keys.
Found lots of dead end threads on the matter, particularly about this issue and people trying to add the remote start function... nothing conclusive... makes me think its back to the two keys issue...
I now have three programmed keys, one which came with the truck (three button) which was the original spare, along with two remote start (four button) OEM keys which start the car but no working buttons. There's a erase keys function on the Autel MK808BT which I haven't tried yet, activated customer key programming and turned unlimited keys mode off, the two keys thing you cannot overwrite... but you can do the erase keys option on the unit.
Renewed the subs on the Autel unit, will check with their service and background stuff over the weekend... don't want rush it and risk ending up with a dead truck. It starts and drives with no MyKey restrictions now, so apart from being annoying, its not desperate.
Will be sure to update this thread when done... nothing worse than googling dead ends, or even searching for them in the forum itself. If anyone has come across and fixed this please let me know.