Plex Server does not see my .flac files in Ubuntu. Files are shown be grayed out

The individual files are always grayed out in that interface, because you can only select folders there. So that’s normal.

As to why Plex isn’t finding flac files: From what I can see in your screenshot, it looks like you have a lot of files from multiple artists in a flat folder. That is only going to work if:

  1. Plex is configured to use the ‘Plex Music’ agent, and
  2. ‘Prefer local metadata’ is enabled, and
  3. your embedded tags are meticulously correct.

If any of those conditions aren’t met, Plex depends heavily on the folder/filename structure of your media files, and they need to be organized in a way that Plex can recognize. In this case, Plex may have found the flac files, but it incorrectly cataloged them in one or more “Various Artists” albums somewhere. You might be able to confirm that by viewing your Library in Albums mode, sorted by Date Added.