I was looking at the wrong place! Issue was not comming from the runner but from SONAR itself. I had to change de sonar config file '/opt/sonar' and restart it. In the setting page I now can see that sonar is running on mysql. I'm facing a other issue with the runner, but it is not related to the issue above.
So basicaly make sure both SONAR and SONAR-RUNNER are configured to work with mysql.