In the /etc/apache2/vhosts/Vhosts_ispconfig.conf there are 2 lines per domain by default that conflict with common dircectories used by CMS Software. So when I go to http://dannyweaver.com/users/login.php I get a 404. I use Genu for my personal site. While its easy enough for me to comment the second line listed above, most users cannot do this. I don't think Genu is the only CMS that uses the users directory in its structure and it would be better if ISPConfig used a less common name. I'm sure "ispusers" would work fine for 99.9% of people. Also, I've been unable to figure out why these aliased dirs are there in the first place. Lastly, you guys do a great job on ISPConfig, and I just sent off my email to join the Development Crew to help with Translation as I speak English, French, German and Esperanto. I'd love to do an Esperanto translation Unfotunatly none of my secondary languages are strong, but the English translation of ISPConfig seems to be weak and that is where I wish the lend a hand the most as it is my native language.
If you don't need those two Alias lines, you can disable them by changing the make_vhosts() function in /root/ispconfig/scripts/lib/config.lib.php.
I had the same problem, and the solution didn't work. What I found out is that at least in 2.2.6 and probably all later versions you (also?) need to edit /root/ispconfig/isp/conf/vhost.conf.master and comment out the AliasMatch lines And might I add that it would be great if this would be a configurable option through ispconfig web interface