Which mysql version are you using?
We have a documentation about mysql/JIRA integratation that can be found on this link:
Have you tried the steps on the documentation?
If you follow the documentation and it does not work, please open a ticket attaching the JIRA logs on it.
I had the same problem when I switched my DB from the internal HSQL to MySQL. I solved the problem with the steps described at: https://confluence.atlassian.com/display/JIRA061/Switching+Databases
(i.e., I erased dbconfig.xml and restarted JIRA)
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