Maybe this will help:
Check in karaf if there is any stable config parameters for mysql & jdbc
config:list "(service.pid=org.openhab.mysql)"
config:list "(service.pid=org.openhab.jdbc)"
If there are wrong stuff there, delete the stored config:
config:delete org.openhab.mysql
config:delete org.openhab.jdbc
Fix your .config and .persist files and let OH2 re-read them to populate the stored configs.
Oops… I missed that part:
You mean that your /etc/openhab2/services/mysql.cfg file is being updated by OH2? (this shouldn’t happen…)