When I go to: ISP Manager - Site - User&Email - User - Advanced Settings There's a textfield 'Message' but no checkbox to enable or disable this auto respond. When I go to https://my.server.com:81/mailuser/ I can activate the auto respond option.
I just tested it with the latest dev branch and the checkbox shows up. I recommend that you upgrade your installation to this version: http://www.ispconfig.org/downloads/ISPConfig-svn-current.tar.gz The current SVN version will be released as ISPConfig 2.3.3 in the next days.