As you say the correct websites loaded the first time you checked them, I can assume it is working correctly and you have a local caching issue on the PC used to view the websites. What happens in your web browser if you 'force' a reload from the server by hitting <Ctrl>+<F5> ?
If you used the "Perfect Server" guide to install ISPConfig, Squirrel Mail should be available on "http://ip.address/webmail"
If you browse to that address, do you get the login page?
If you want Squirrel Mail to be available on a virtual domain, you need to make the symbolic link in the correct place, eg:
ln -s /usr/share/squirrelmail/ /var/www/domain.tld/web/webmail