[Milhouse]

OK, I kept trying, and this issue seems to be related to the way Kodi recognizes/catalogs the episodes or movies, and then opens the subs file in accordance to the filename (or DB name).
Example: I open an episode from the TV Shows listing, no subtitles shown, then I try opening the very same episode from the files section, the subs appears.

I would suggest you open a ticket on trac.kodi.tv, and provide a sample subtitle file so that this can be reproduced - just the subtitle file should be sufficient, as I'm assuming it can be used with any video file. Include details of the exact file naming conventions you are using (for both the video and subtitle files). A debug log (wiki) should also be provided.