Hiya guys, after a quick test, I found that removing the pylon fully (not just the payload i.e. the fuel tank) fixes the issue of it not adding fuel to the system. After removing the tank without the pylon no change would be seen when adding it back however, removing the pylon and then adding the tank made the fuel jump from 7100 to 9000.
Thanks burner1111 for mentioning your experience or I wouldn't have thought of this. As well as everyone who went out of their time to comment.
