That's a different pedal port. This doesn't reveal anything about what FC1 Pedal 2 might configured to do.
What is "Output 1 Volume" set to in the Setup: Midi/Remote: Other menu?
That was where I went wrong. Somehow I missed scrolling that row of tabs to the Other menu. The output was as you suspected so I changed it to NONE and now it works fine.
I'm guessing I thought the #3 and 4 jacks were 'not working' due to my wrong choices.
When I received the AxeFx III, used, the Wah just worked right away by plugging in to FC Pedal 1.
I picked External 1 and it worked, dumb luck, I'm the blind squirrel that found a nut. I was only getting results from jacks 1 and 2 since they were assigned to External and 3 and 4 were not. I was using the wrong Pedal choice to assign them to modify things by picking 'External Pedal' instead of 'FC Pedal'....
The Wah was already working and it used the the External Pedal choice ( of course Pedal 1 wasn't also assigned to the output volume in the Other menu) so I thought the same thing should work for the Rotary by choosing External Pedal 2. It was controlling both due to the Assignment you pointed me to in the Other menu...
Coming from the Ultra and then the IIxl+ I thought I didn't really need to read the whole manual for the III...lol...when the FC in AxeEdit seemed to have eliminated the need for menu diving assignment for modifiers etc. because the Wah worked without diving in so I made a bad assumption...
Many thanks! It is all good now!
I just want to say I have been an on again off again user of the AxeFx since the Ultra came out and I sold the Ultra and then the IIxl+ to get a more friendly user interface, the need for more outboard devices connection/routing options and better foot control that the competitive devices had.
Now I'm going to sell those others because the new improved Axe Fx III with FC-6/12 has made the compromise unwarranted. It is so good right now I feel guilty having this much at my disposal! And the amps and cabs sound really, really, good too....I swear it isn't just confirmation bias...it really is significantly better sounding than the IIxl+ was