Multisite alternative uploads folder doesn't generate thumbnails

For a WP multisite that I’m working on I have an alternative uploads folder called “uploads-blog”. Since upgrading to WP 3.5 I can’t seem to get WP to generate thumbnails for the uploaded images in that folder any longer. Whenever I upload a new image to the alternative site only the original image is uploaded. The base site, which uses the regular uploads folder, works. Is there a setting or a function that I am missing in order to get this to work with the new version of WP?
Currently running version 3.5.1.

In .htaccess –

RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# uploaded files
RewriteRule ^files/(.+) wp-includes/ms-files.php?file=$1 [L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule . index.php [L]

In functions.php (for the alternative site’s theme) –

add_theme_support( 'post-thumbnails' );
add_image_size( 'default', 610, 999 );

Edit: I’ve noticed that WP now uses the Files folder for alternative uploads instead of my custom folder. While this works (no broken images) it still doesn’t generate any thumbnails for them.