Database corruption is easy to spot. Look in the Plex Media Server.log files (same as mentioned earlier). You’ll see entries similar to ERROR - SQLITE3:(nil), 11, database corruption at line 64817 of [bf8c1b2b7a]. Warning level entries are typically not a problem.
You’ve performed the Plex Dance, so that takes care of emptying the trash and cleaning bundles. Perform a database optimization as well.
Post your server logs and we can see if there is anything interesting. Post the entire ZIP file. The Plex Media Scanner or other files might have useful info as well.
