Adding a main folder to a Library vs individual subfolders

I have been using Plex for about a year and like it very much, but from time to time I see the where media stops showing up. I end up rebuilding my Index usually when this happens but notice that it seems to make a difference whether I add a single folder as my Library or I go in and individually add the higher level sub-folders of that single folder. It seems that if I just add the single parent folder PleX skips the sub-folders for the most part. I have read through the following link but it does not seem to address this other to recommend my less effective method of listing the parent folder: https://support.plex.tv/articles/200381023-naming-movie-files/

Has anyone seen the same behavior that I am seeing? I am running PleX on Windows 10. Thanks!

I have zero problems using a pretty large library with a single folder with subfolders and even subfolders in the subfolders.

It should be noted that I do NOT use single folders for each movie and I do not want or need the extras or other benefits that brings. I just watch movies.