Anyone got a solution to this one we are having the same problem also and it is driving us mad. All our sites were saying permisison denied at one stage.
What version of Plesk are you using?
We are using 7.1.1.
Also we now appear to be having this issue on protected directories also. (Did anyone else install Nagios by any chance?)
I think it was Nagios that stuffed things up for me and it looks like the following script in the RPM did it;
preinstall scriptlet (using /bin/sh):
if ! /usr/bin/id nagios &>/dev/null; then
        /usr/sbin/useradd -r -d /var/log/nagios -s /bin/sh -c "nagios" nagios || \
                logger -t nagios/rpm "Unexpected error adding user \"nagios\". Aborting installation."
fi
postinstall scriptlet (using /bin/sh):
/sbin/chkconfig --add nagios
if /usr/bin/id apache &>/dev/null; then
        if ! /usr/bin/id -Gn apache 2>/dev/null | grep -q nagios ; then
                /usr/sbin/usermod -G nagios apache &>/dev/null
        fi
else
        logger -t nagios/rpm "User \"apache\" does not exist and is not added to group \"nagios\". Sending commands to Nagios from the command CGI is not possible."
fi
if [ -f /etc/httpd/conf/httpd.conf ]; then
        if ! grep -q "Include .*/nagios.conf" /etc/httpd/conf/httpd.conf; then
                echo -e "\n# Include /etc/httpd/conf.d/nagios.conf" >> /etc/httpd/conf/httpd.conf
#               /sbin/service httpd restart
        fi
fi
Unfortunately I can't work out which part did the damage.
http://www.netvantage.com.au