File association only has to do with which program is used to play the file when it is executed outside of JRiver in a Computer or Windows Explorer window.
The files should show up in JRiver regardless if they have metadata or are configured to be properly processed or played. The only filter for whether DSD files show is a checkbox for DSD Audio, which includes all DFF, DSF and SACD, regardless of bitrate - and you obviously have that enabled if you're seeing other DSF files.
If you're using Auto-Import, are the double DSD files in a separate folder from the other DSD files, and if so, is that a subfolder of an existing watched folder or a separate Auto-Import entry? If it is a separate entry, is file type DSD Audio checked and is the Mode selected to Include rather than Exclude in the folder options?
Where are you viewing the files? Are you looking in Audio > Files > Drive|Folder rather than the Album, Artist or Genre folders under Audio?
Steve