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Hi,
The issue is caused by carbon cloning of the search element within the header. When I start scrolling a duplicate copy is made via a custom script of the search and I guess that is used within the scroll window: https://i.imgur.com/HLDV3zO.png
That is a very bad practice, and usually causes major issues. I designed the plugin to try to resolve these if possible, so that is why the plugin does work initially, but the isotope script fails at some point due to bad variable pointers. I’m afraid I can’t do anything about that from the plugin perspective, as the whole script would have to be deconstructed.
The best and easiest solution would be to use a different sticky header script, which does not use a javascript clone mechanism.