There are two things you can do.
To disable UpdateMedia (the application which indexes your media everytime you reboot), you'll have to go with mysql in pluto_main database and find in the table StartupScript a record with Command = "UpdateMediaDaemon.sh". Delete that record.
The mysql error is very weird, because mysql should be able to store millions of records. You can cleanup pluto_media running these sql queries:
DELETE FROM File;
DELETE FROM File_Attribute;
DELETE FROM Attribute;
DELETE FROM SearchToken;
DELETE FROM SearchToken_Attribute;
However, we would like to see what's exactly wrong there, so please don't forget to send me a private message with your password for remote access. Also be sure you have no external firewall blocking 24388 and 24389 ports.