Tim in melbourne wrote:
...Any idea what might be going on?
I'm looking at the last picture in the first post from Andybighair, in the thread from the link that you provided. To start with, the drawing in that thread has the numbers wrong, it shows position 1 as the neck. Position 1 is always the bridge position (switch knob towards bottom of guitar). Looks like that whole thread is full of confusion.
Using the drawing in that thread, if you wired the tone pots to the yellow terminals labeled 1 and 4, then you should have one tone control on the "neck" position only, and the other tone control on the "bridge/middle" position only.
In your original post, you indicated that you wanted tone control on the "bridge only". How exactly do you want your tone controls to work?
Standard Strat wiring gives one tone control for the neck, and one tone control for the middle, with the bridge having no tone control. My drawing has one tone control on the neck, and one tone control on the bridge, with the middle having no tone control. With the super switch, there are many other options, just figure how you want yours to work first.