Regarding the PHP notices:
You seem to use php 5.3 and have a wrong error reporting Level set in your php.ini file.
Please set error eporting to:
error_reporting = E_ALL & ~E_NOTICE | E_DEPRECATED
error_reporting = E_ALL & ~ E_NOTICE & ~ E_DEPRECATED
in php.ini and restart apache.
Regarding the repquota warning, you missed to install the quotatools package insider your servers which contains the repquota command. Quotatools are required by ispconfig.