The footnotes in that page that aren't parsing appear to be using a template called "foot book", which is intended to insert a FOOTNOTE BB-Code. However, the template has syntax like:
Code:
[footnote[if="{{{1}}}"]={{{1}}}[else /][/if]]
As you can see, the IF is attempting to modify the tag portion of the footnote (before the equals sign), rather than the option portion (after the equals sign). This may have worked years ago in vBulletin, but it conflicts with some security aspects, and is not possible at all in XenForo. I can't be sure that it is the only problem, but it definitely isn't helping.
You will want to place the IF on the outside of the footnote tag, with two copies, like:
Code:
[if="{{{1}}}"]
[footnote={{{1}}}] ... footnote content ... [/footnote]
[else /]
[footnote] ... footnote content ... [/footnote]
[/if]
To avoid duplicating the code inside the footnote tags, you can consider using local variables:
Code:
[var]set|footnoteContent| ... footnote content ...[/var]
...
[var]get|footnoteContent[/var]
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