There are a few places you need to look to make sure the FC7 can control superknob. That said, I'll list some extra things to be complete of why one may find the FC7 doesn't control superknob like they think it should.
1) By default, the presets are programmed to "link" superknob with an FC7 plugged into the FC2 port (there are two "FOOT CONTROLLER" ports on the back of Montage labeled 1 and 2. Shorthand for this is FC1 and FC2) Note: the foot controller can be plugged into either port FC1 or FC2 and still control superknob. However, this has to be programmed - and assuming you use some presets (without modification) - why not stick with the convention and generally use FC2 for your superknob control? So this is the "is it plugged in" kind of check - and FC2 to use default programming.
2) When you load a compatible file from say a Motif XF or MOXF or any of the past synths/workstations that had no concept of superknob - keep in mind that the conversion process does not "inject" the new Montage convention for FC2 controlling superknob. A recent conversion I did, loading an X3A (Motif XF "all" file) into a library programmed Foot Controller port 2 (FC2) to CC4 which is standard for "Foot Controller". So if you are using a performance that is loaded from a previous generation and expect the foot controller to control superknob, check your FC2 control assignment. See the step "4)" for this. Also keep in mind that even Montage content may "flub" or go against convention if you load libraries from 3rd parties or even Yamaha. Although the internal presets follow this convention - even Montage-targeted content can break this convention. And certainly if you get user content - there's no telling.
This step is a general "consider the birth of your performance". If it was "born" from a preset - meaning you "copied" ( [STORE] and edited version of a preset in the user area) a preset - then chances are it will be following convention unless you changed one of the settings mentioned in this checklist. If the performance was "born" from non-preset content (like loading something off the net or made for a previous keyboard) - then chances are this content will not follow convention and you will have to edit parameters to suit.
3) Utility "global" settings Checklist: Since firmware v1.20, superknob has been able to be changed from SysEx to a CC number of your choice. The "default" CC choice is 95. Or "off" for the previous firmware's method of using SysEx. Rather than arbitrarily setting this - just make sure this value is not changing and check it from time to time as a sanity check. Chicken and egg - if you're having a problem it's hard to know if it's changed and that's the issue. If it isn't set to "off" or "95" - then there may be an issue. At least you are not looking at default.
To edit these, press [UTILITY], then touchscreen (TS) left-hand menus "Settings" -> "MIDI I/O", then TS "Super Knob CC" set to Off or 1-95.
4) Parameter Checklist: Press [PERFORMANCE] (HOME). Then press the [EDIT] button. Then user the touchscreen (TS) to select the left-hand menu: "Control" -> "Control Number". Assuming your FC7 is plugged into foot controller port 2 (FC2) - look at "Foot Ctrl 2" and ensure the setting is set to "Super Knob". Whichever port you think should be controlling super knob needs to be set to "Super Knob". If it does not say "Super Knob" then you need to highlight this area and spin the data dial until the box reads "Super Knob".
5) Parameter Checklist: Go to the first PART (highlight/touch PART #1 from [PERFORMANCE] (HOME) screen) then press the "Edit" option from the touchscreen. Then select the menu (with "Common" in the lower-left corner selected) the menu "Mod/Control" -> "Receive Sw". Check the settings. If your superknob is controlled by CC messages, then it's possible that these CC messages could be filtered by turning the CC "off". Or you could go back to step "3)" and set superknob CC to "off" (use SysEx) which would make it "impossible" to turn off the FC control of superknob.
6) More crazy stuff: check to see you do not have multiple controllers assigned to the same CC. Again, making superknob CC "off" (user SysEx) would clear this up. But if you pick a CC for superknob that is used by something else - you may get unexpected results.
7) If all else fails, save everything (backup) and do a factory reset.