Russian description at http://blog.scopenco.net/ispmanager-plugin-diraccess/
There is a bug in ISPmanager with scheme where nginx and apache+itk is used. Private directories are not accesible because config files passwd and .htaccess are created with wrong permissions. This plugin fixes the problem.
cp -v etc/ispmgr_mod_diraccess_fix.xml /usr/local/ispmgr/etc/
cp -v addon/diraccess_fix_perms.py /usr/local/ispmgr/addon/
killall -9 ispmgr
Tested on CentOS 6.
If you have questions or problems getting things working, first try searching wiki.
If all else fails, you can email me and I'll try and respond as soon as I get a chance.
-- Andrey V. Scopenco (andrey@scopenco.net)