I have moves and series sorting set to the following.
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%dn/%dn.%ext
In 4.0.2 the same 'Show.Name.S01E01.1080p.AMZN.WEB-DL.DDP5.1.H.264-NTb.nzb' is sorted to '/downloadFolder/Show.Name.S01E01.1080p.AMZN.WEB-DL.DDP5.1.H.264-NTb/Show.Name.S01E01.1080p.AMZN.WEB-DL.DDP5.1.H.264-NTb.mkv' with no other changes in settings.
Rolling back the same installation from 4.0.3 to 4.0.2 fixes the issue. Going back to 4.0.3 brings the renaming issue back.
I am running from source on Ubuntu 20.04 in a Python 3.11.4 virtualenv. All Python dependencies are updated from the requirements.txt file.