I did see this once, IIRC, before this report, but I haven't managed to reproduce this now. It's very possible we fixed the underlying bug (which is probably just a missing call to recalculate the behavior of this sidebar after page changes).
The situation has improved, and most of the time the issue can be solved by simply scrolling around now, but it's not completely gone yet.
One trigger is the following:
Open up the style properties overview
Scroll to the bottom of the page
Close the navigation category
Half of the page navigation will now be unreachable, as it is clipped out of the page. It works on various other pages as well, and depending on the height of the category, it will either clip out at the top, or the bottom.
That issue should be fixed now and it's quite possible the original bug was a somewhat similar issue. This was a bug in the underlying sticky kit library we use for this sidebar, though it's something we've forked with some tweaks already so I was able to identify the cause and fix it (ironically, what looks like a quirk of CoffeeScript compilation).