Do you use any rewrite rules in this aliasdomain? Scripts will only work if no rewrite rules are used (the aliasdomain is not forwarded to a subfolder). If a aliasdomain shall have its own folder, then better create a new website instead of using a aliasdomain.
With Fast-CGI and other php-modes it works. Looks like your rule in vhost changed directory and cant find php-cgi anymore.
