I have installed several MultiSite's and there is a difference but I can't figure out what it is.
Basically, if I want to run a script like timthumb (or any custom php script that exists "outside" wordpress) I can't reference that file.
For example I am trying to access the thumb.php script I have in my theme directory. Here's a screenshot to prove that it is uploaded:
Here's the link to it not working (and instead giving me a "Page not found" 404 error):
The same thing happens when I try it with any custom PHP file. (EG: using the script found here: http://wpengineer.com/1038/embed-wordpress-functions-outside-wordpress/
However, I also have WP Multi Site installs where it DOES allow me to access custom PHP files. I have looked through all the settings, .htaccess file and wp-config files to see if there are any differences and they are identical to the non-working MultiSite installs.
I am wondering if it is a permission problem of some kind because I can access image files (example: http://mintthemes.com/wp-content/themes/MintTheme/screenshot.png
But I can't access PHP files directly using their URL.