Why is PHP's register_globals option is enabled??? Thats rather unsafe, any person has access to MediaWiki's source code, If they find one mistake in the way vars are handled they could get your admin password using an xss exploit?
As far as the page not working, what is the page you expect to work?
site.com/wiki/index.php
is error reporting turned on in php.ini if index.php exists it should atleast throw some errors? The only other thing I can think of is did you modify MonoBook.php? or index.php in some wierd way? I had added a html comment under the </html> tag on my MonoBook.php file once and it gave me simular trouble to what you have: sometimes only page headers would be sent, no page content.
Chris