What I want to know first is did you click the correct AutoMagic buttons for your Network / Multisite site type and activate BulletProof Mode on the Primary site ONLY?
Next do you see this .htaccess code below in your root .htaccess file? If so, delete it or comment it out with # signs as shown below.
#RewriteEngine On #RewriteBase / #RewriteRule ^wp-admin/includes/ - [F,L] #RewriteRule !^wp-includes/ - [S=3] #RewriteRule ^wp-includes/[^/]+\.php$ - [F,L] #RewriteRule ^wp-includes/js/tinymce/langs/.+\.php - [F,L] #RewriteRule ^wp-includes/theme-compat/ - [F,L]
Next did you create RewriteRules like these shown below at any time for this Network / Multisite site?
RewriteRule ^blah1/files/(.*)$ http://www.example.com/wordpress/wp-content/blogs.dir/5/files/$1 [L,R=301] RewriteRule ^blah2/files/(.*)$ http://www.example.com/wordpress/wp-content/blogs.dir/6/files/$1 [L,R=301]