We are working on some file browsing functionality that should help with resolve these cases in a faster, more transparent and intuitive way, but for now this does sound frustrating.
This would be my guess too, but it sounds like you tried the usual methods for ruling this out so I’d like to take a stab at reproducing this @AndersVinberg.
Anything we need to know to replicate your setup as closely as possible? This is a Windows Core? What kind of storage device, and how is it added?
Can you PM me a link to the files in question, too? Might as well be testing with the same media.