Nothing is wrong. This is normal. Here is what is happening and why:
The FC7 is not motorized. Therefore, it physically remains wherever you leave it.

If, for example, you leave it in the toe-down position, then change Performances, and this new Performance has the Super Knob stored at minimum. In order for the physical pedal to begin working you will need to “go get it” (referred to as “hooking” the value). You must return the pedal to minimum (heel-down) before it becomes active.

If the pedal had a motor it would follow the Super Knob — but that is not going to happen.

Extra Credit:
The Sliders work the same way... the Sliders are not motorized, either. A Slider is inactive until you move it through the ‘stored’ value. You can see this in the screen when viewing the split screen with the “Element/Operator” Levels and Switches showing on the right side.

Here’s an example, recall the Single Part Organ Performance “8.8.8.8.6.2.2.0.0” (drawbar Settings are on the sliders)
The screen is split showing the “Part1 Element Sw/Level” on the right hand side.
Close inspection you will see little blue chevrons (arrowheads) indicating where your physical sliders are presently located and you can determine which ones are currently active 1-4 or 5-8.

If 1-4 are active the chevrons will appear next to those sliders
When 5-8 are active the chevrons will appear next to those sliders
You can switch that with the [Element/Operator] button that toggles 1-4, 5-8

The chevrons will be blue *until* you move the physical fader through the stored value... as soon as you reach that value the chevron will turn white — indicating it is now active. It passes through the stored values and ‘hooks’ it (engages it).

This hooking method is fairly standard. The other alternatives are motorized devices, like a Yamaha digital mixers where the faders move automatically to the stored values (not practical on a synthesizer) or the value ‘jumps’ to wherever the controller is physically (this, as you can imagine, can be catastrophic from a musical point of view).

As concerns the Super Knob... its position can be stored. It is programmer’s choice about where the Super Knob is ‘stored’.
Recall “CFX + FM EP 2”
When first recalled the Super Knob is at minimum value (regardless of where your FC7 is physically) minimum recalls the CFX acoustic piano. You must move the pedal to the heel-down position to activate it, once active you can morph the CFX acoustic piano to the FM electric piano.