Most common issues with files not showing up where you expect them are permissions or bad naming. Make sure the system account used by Syno to run your PMS has access to the media not showing up! → Synology FAQ - Questions, Answers, and How-To's - #25 by ChuckPa
A movie library will e.g. ignore items named like a tv-show or unsupported formats, such as disk images.
https://support.plex.tv/articles/201543057-why-is-some-of-my-content-not-found/
Plex doesn’t usually like it if you have additional tiers of folders to the expected organization schema (such as grouping your music by categories).
If you must keep the extra layers, you can e.g. treat each of those category folders as a library folder of its own.
Example
Folder structure
Music
Jazz
Artist A
Album 1
...
Blues
Artist B
Album 2
...
Album 3
...
Rock (Old School)
Artist C
Album 4
...
Instead of pointing your library to Music, point it to the individual category folders (and only to those!!); each library can be pointing to multiple folders… just make sure to avoid cross-references (e.g. by pointing to Music and some of its child directories). Based on the above example, you’d be pointing your library to :
Music/JazzMusic/BluesMusic/Rock (Old School)