I experienced something similar few months ago. After a long time debugging I found out that all the problems were related to this well hidden option called:
ms_files_rewriting
in the wp_sitemeta table. It was active in my case, with the value 1.
When active, WordPress assumes you want to use the deprecated blogs.dir structure, where the files are served through the ms-files.php file.
I wonder if that’s causing your problem.
At least check the value of this site option, and if it’s active, try to set it to 0.
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