Assuming that you are only using local storage and don’t spin down your disks, then you have a hardware problem with your storage.
Only other thing I can think of is if you have another program that is accessing the Plex database and holding a lock to long. Restore the last backup and see how it goes.
https://support.plex.tv/articles/202485658-restore-a-database-backed-up-via-scheduled-tasks/
You should update: Plex Media Server - Security Update
