Files permissions problem, only without "www" prefix

Hello all,
I made some changes in my server(changed domain, upgraded ISPconfig etc.) and suddenly I've noticed that all of the websites stored on my ISPconfig (3.0.5.4p5) that needs some file permissions, can't activate them.
(Here is an example of an error:
Warning: fopen(/var/www/clients/client5/web7/web/dev/basis/logs/db/29_03_2015.log): failed to open stream: Permission denied in /var/www/clients/client5/web7/web/dev/basis/helpers/basic/Logs.class.php on line 179 )

BUT,
If i enter the same address with "www" prefix, it works great(!)
Where did I screw up?

Thank you very much,
Tzahi.

 

It was already installed and enabled,
Thanks for the quick reply.

 

Yes.

 

php mode is fpm.
rebooted couple of times

 

No, same problem here. also tried to restart apache2.