I'm having the same problem, upgrading from 0.5 to 0.6
The installto.sh does not work, arguing that suhosin.session.encrypt is incorectly set. It is however correctly set in the .htaccess of both the 0.5 and 0.6 roundcube folders. But it is on in my /etc/php5/apache2/conf.d/suhosin.ini file (debian squeeze), something I want to keep that way.
I guess the script relies on reading the global config file, rather than the .htaccess. I've tried to bypass that check, but did not found it in installto.sh
Any idea ?