My pedal is set to globally control the output volume - thanks
Are you sure you don't have it controlling the input?
From the manual:
GLOBAL VOLUME PEDAL SETUP
The Axe-Fx III allows remote control of the volume at all inputs and outputs. If you have a second pedal, or if you
want to use one pedal for global volume instead of expression, follow the instructions below:
The first step is to decide which volume you want to control. Adjusting Input volume affects gain/distortion and
the behavior of level-dependent blocks like the compressor or gate. Adjusting Output volume does not affect
level-dependent blocks, but scales everything you hear including effect tails. For all other volume options, you can
insert a Volume block anywhere in your preset and control it with an “External Controller” as described above
(See also “Modifiers” on p. 53.)
To set up a global volume pedal, first ensure that you have a pedal connected and ready to use. Then:
1. From the Home page, open SETUP: MIDI/Remote: Other.
2. NAV to the entry for the volume you want to control: Input 1, 2, 3, or 4, or Output 1, 2, 3, or 4.
3. Turn the “A“ or VALUE knob to assign a controller to your selected entry.
Select “PEDAL 1 or PEDAL 2” for the onboard Expression jacks
Select “FC__ PEDAL __” for a pedal connected via an FC series controller.
Select a number if your pedal is transmitting a MIDI CC#. For example, by default, the Fractal Audio
Systems MFC-101 transmits CC#11 for XP1 and CC#16 for XP2.
4. Test and EXIT when finished.
Learn about other options for global remote control in “The MIDI/Remote Menu” on p. 73.