Can you upload some of your server logs? Folks will definitely wanna see those to get more details about what your server is doing since others aren’t having this problem and that’ll provide insight for them (I’m not good at reading them but others are).
Can you detail your server setup a bit more? I’m not sure I understand the dual server situation. Do you have different media stored in two locations or same media in two locations or media in one location but two different Plex Server instances? That kinda thing is unclear.
It’s likely not a permissions issue since a manual scan is fine.
But since the manual and scheduled scan is fine it makes me think about something else. I know there is a file limit on the auto scan - if you have too many files then there’s a limit file systems can hit where OS won’t notice new files automatically anymore which is what triggers the auto scan. It’s a pretty big limit but folks with music and\or photo libraries can hit it. I can’t find it right now though… my search-fu is failing. But it might help if you share how many files you’ve got and how they’re organized. Someone else will know the limit I’m talking about and can say if it applies or not.
EDIT: I think I found it: Synology FAQ - Questions, Answers, and How-To's - #22 by ChuckPa - says Synology but impacts all linux setups.
