Sometimes when something is wrong, ISPconfig cannot generate a proper vhost file. In that case, the original file remains linked to the sites-enabled directory, but a second, newer vhost file with a .vhost.error (or something like that) extension is created in the sites-available directory.
You sure you do not have one in there?
Next step I guess would be to enable DEBUG logging for your server (under system) and see what it logs when you update the site.
Last edited by anset; 19th February 2012 at 22:54.