All sorted.
The SkyLink system replaces broken HomeLink remotes.
Essentially it is a new remote control unit that doesn't use the HomeLink system.
You wire a device on the wall that replaces the standard button that comes with the garage opener.
That is a receiver, the new SkyLink remote connected to that receiver and causes the button to be pressed.
So it never sends a signal wirelessly to the opener, only to the wall button.
That's why I couldn't program the car with the SkyLink remote.
So I swapped the SkyLink system over to the other door and used the original remote to program the car - job done!!
Thanks for the help.