Ah yes, the problem is because by default the script only scans direct children nodes of the pagination container for special links (ie: those with class="toc"). When you added a list, the links are no longer direct children of the DIVs, but the LIs instead.
To fix this, find the below lines in red in the .js file:
Code:
config.$toc=config.$togglerdiv.children('.toc')
config.$next=config.$togglerdiv.children('.next')
config.$prev=config.$togglerdiv.children('.prev')
Replace the part in red with "find" instead (no quotes). I've updated the .js file officially on the script page as well btw.
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