We ran into that problem on our internal development server ( ubuntu ).

Our test sites were all running into problems, permissions and ownerships seemed to be ok.
But the /etc/log/apache2/error.log contained the following error upon opening such a test site:

pcfg_openfile unable to check htaccess file

Problem was a little typo in /etc/group. The apache user contained a “0″ ( zero ) where a “w” was due.
The 0 was inserted when we edited the file to add a new user to a group on the server.
After the typo was fixed, a quick reboot of the apache server was needed to get things to normal.