Hi Mustafa,
So, don't reset mysql root password except from kloxo script and or from panel.
I did reset the mysql password from the command line.
Before I did this reset, all mailboxes got created in the main root directory of centos, like /etc, /user_mailbox1, /user_mailbox2, /usr, /var, ...
This should not happen.
When this happened, it could not connect to mysql. It could connect with mysql only after I made a reset of mysql root password from command line. There is something wrong in fixmail script which should not create mailboxes like this.