How are you trying to set up the associations?
The way I do it is...
1. Run Windows Explorer
2. Navigate to the file you want to associate
3. Right click the file and select Open With
4. Select Choose another app
5. Check Always use this app to open .epub files (or whatever file type your file is)
6. Select More apps
7. Select Look for another app on this PC
8. Navigate to the Calibre eBook viewer
9. Once you've navigated to the Calibre directory, select ebook-viewer.exe
10. Click Open
11. Done
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