Two things come to mind as a starting point before others jump on this thread …
- You say your server is
latest as of yesterdaybut can you confirm the number. Version1.25.6.5545has scanner fixes which caused some folks problems with previous versions so it might be a factor. - With 400+ episodes are all these in a single folder or have you broken them up into seasons specific folders? The plex scanner is more efficient when your media is in season folders so maybe with this number of episodes you could be having problems.
Outside of that its hard to guess so maybe a copy of your full server logs after a plex dance might be good and a directory listing of the files on disk would be useful to check.
