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 virtfs, jailshell copies all mountpoints
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?