Multisite media mapping issue

I’ve just started to migrate an older multisite network to fresh install. I’ve installed it using the “subdirectory” option, then used the Domain Mapping plugin to map another domain to a subsite.

Currently, I have:
main-site.com
secondary-site.com (a domain mapped to main-site.com/secondary/)

Permalinks on the secondary site are working fine, but URL rewriting isn’t working for media uploads. All uploads are accessible only via the main site.

mainsite.com/secondary/wp-content/uploads/sites/2/2013/07/image.jpg

Here’s the .htaccess rules I’m using:

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

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule . index.php [L]
# END WordPress

Any ideas as to why uploads aren’t being routed through ‘secondary-site.com/files/*/*/image.jpg’?