Without seeing the logs from when PMS starts, I’m going to suspect that you have a lot of media (music, photos, tv series) which you’ve properly curated all into nice clean subdirectories.
If this is the case, the default table limits in Linux are interfering and blocking the automatic detection (the table is full).
There is a procedure for synology to determine if this applies to you and, if so, how to tune your Synology to allow for more directories to be monitored by PMS.