I upgraded from 1.5 to 2.0.1 yesterday. My main installation is in /blog/wp/. The index.php inside that directory works fine. I have 3 other index pages around my site that previously (pre-upgrade) contained posts from certain categories. /asperger/index.php, for instance contained the WP header and contained posts pertaining to that topic.
As long as I actually call it like http://www.ponderethereal.com/asperger/index.php, it works ok.. but if you go to http://www.ponderethereal.com/asperger/, it gives the following message :
"The requested URL /cgi-sys/php-fastcgi/test/index.php was not found on this server."
If you remove all things wordpress from the index, it works fine. For instance http://www.ponderethereal.com/tangible - so it is something in wordpress causing it.
While it is inop, I have adjusted the asperger page to remove all things wordpress... but you can see the issue duplicated here : http://www.ponderethereal.com/test and you can see it working properly here :