Comments - Changing location of database
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Silly question, but you said you stopped the database, reset the basedir in your my.cnf, and then restarted... did you move the data in the datadir to the new location?
Yes, I did. Also ran checktable on every table. Since writing I have also dropped all schemas and recreated them from scripts. Again all ok until I reboot. Thinking it could be to do with permissions because linux sets all permissions on NTFS drives to root and everybody. Does not use sudo or mysql accounts and doesn't allow them to be changed.