Both tone pots work the second one just not with the humbucker selected alone.
If you've used the Duncan diagram as it is, the bridge pickup doesn't have a tone pot! Only the neck and middle pickups have tone controls, like a vintage Strat.
If you want the bridge pickup to share the middle pickup's tone control, you need to wire a short "jumper" lead between the second and third terminals of the 5-way switch,on the side facing the controls (i.e. the terminal connected to the outside tone control and the "spare" one next to it)
As for the volume pot could I have overheated it so it's not working properly?
It's possible. I've fried pots before!