Yes, there is something that you are missing. What you described is the correct way that PitchFactor works, but you must understand that Bank Up does not actually change sounds. It just cues the next Bank of Presets so that you can use the Left or Middle footswitch (in Bank Mode) to select a new Preset.
Here are the two modes and what the onboard footswitches do. Remember that you can switch modes by pressing and holding the Right Footswitch for a few seconds.
FS1: Select Bank's First Preset/Bypass
FS2: Select Bank's Second Preset/Bypass
FS3: Bank Up
You can assign an aux switch to do a variety of things. It sounds like something that would work for you is this:
Leave PitchFactor in Bank Mode. Assign the Aux Switch so you have:
Aux1 (Tip): Bank Down
Aux2 (Ring): Flex/Learn
Aux3 (T+R): Tap
Now you can cue up banks in either direction and press PitchFactor's Left of Middle Footswitch to select a new preset.