I later found out that I changed the permissions of the vqadmin and qmailadmin cgi-bin folders thus making the applications not work. There was no effective error but I was unable to login to the qmailadmin interface and the vqadmin showed a lot of strange errors such as: missing domains, domain has no postmaster, etc.
In order to fix these problems the simplest way is to go to their respective source folder and do a make install-strip again. This will also rewrite the .htaccess from vqadmin so it might be wise to back it up if you changed it a lot.