EDIT: Nevermind, I found the solution. I did some Googling, and found that I needed to add a handler to the web.config handler list after the php one I added:
<add name="StaticFile" path="" verb="" type="" modules="DefaultDocumentModule,StaticFileModule,DirectoryListingModule" scriptProcessor="" resourceType="Either" requireAccess="Read" preCondition="" />
Once I did that, loading via default document without explicitly specifying a PHP file worked fine.
Thanks. Clearing the cache didn't do anything. I turned on detailed errors, what I get is:
HTTP Error 404.4 - Not Found
The resource you are looking for does not have a handler associated with it.
(Error 0x80070002)
The default file, index.php, definitely has a handler. I specify it right there in the web.config, and if you put /index.php manually it works. Is there a debugging way to tell what file it is trying to load when it throws the 404.4? Maybe it's not the index.php it is attempting to use.