This fixed it, I edited the file /etc/apache2/sites-enabled/000-roundcube to:
Alias /webmail /usr/share/roundcube
AddHandler php5-script .php
php_admin_value open_basedir "/usr/share/roundcube"
and then the rest there was.
Now it works fine. It might be the "dirty" way, but I think it's better than disabling suPHP all together.
Thanks for your help, I think more people come across this and now have a nice all in one topic solution.