Stickiest seems to be adding a UNION clause to the discussion index SQL, which I don't think Flarum uses natively. Actually, I checked the source code, Flarum uses a similar approach, and Stickiest uses a fork of that. But the code has changed along the years so I'm really not sure how much we can say is identical.
There is a good chance the problem is caused by that extension. Maybe you are able to confirm for certain by disabling the extension or trying if the native Sticky has the same effect, maybe on a copy of the forum.
Reading through the source code I don't see any obvious mistake but the code is very complex. It would probably be useful to add a few integration tests to the extension to verify it works as intended the-turk/flarum-stickiestblob/master/src/PinStickiedDiscussionsToTop.php
