WP 3.5.2 upgrade - can no longer access Piwik in subdirectory (no replies)

Since upgrading WP Multisite to WP 3.5.2, I can no longer access the Piwik installation in a subdirectory. Get a 404 error page. However, I have other OpenCart installation in a subdirectory, and can access it without issue. Can anyone advise how to fix this? Perhaps it has something to do with my htaccess file for WP - or maybe I need one in the Piwik folder?

Any help would be most appreciated!

.htaccess file in root (WP install)

Piwik in subdirectory title "/stats"

# BEGIN s2Member GZIP exclusions
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{QUERY_STRING} (^|\?|&)s2member_file_download\=.+ [OR]
RewriteCond %{QUERY_STRING} (^|\?|&)no-gzip\=1
RewriteRule .* - [E=no-gzip:1]
</IfModule>
# END s2Member GZIP exclusions

# BEGIN WordPress
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]
# END WordPress

AddType video/ogg .ogv
AddType video/mp4 .mp4
AddType video/webm .webm