During CageFS package installation or update all users with jailshell enabled will have it changed to regular /bin/bash in /etc/passwd .
This is done to avoid possible conflict with virtfs when non-cagefs user enters to virtfs, jailshell copies all
If you have mysql-governor installed, all mysql upgrades and version changes should be changed using mysql-governor tools, e.g. http://docs.cloudlinux.com/change_mysql_version.html
On cPanel servers, when ‘mysqlgovernor.py –install’