broken permalinks – site-wide-tags?

Hello,

I support a WordPress multisite installation.

versions:
WordPress 3.2.1 (subdomain multi-site)
Site-Wide-Tags plugin 0.4.0.1 (just now upgraded to 0.4.1.1)
site url: http://ednabrewer.net

Problem: Permalinks often break on main site. Updating permalinks from main site fixes problem, but problem keeps happening. Not clear to me what causes them to break – my working assumption is that it may be caused by a new post to a subsite that is brought up to the main site via SWT.

I’m using site-wide-tags in “main-blog” mode: sub-site posts are published in the main blog.

Main site is using “Day and Name” option under “Common Settings” in permalink settings page. Sub-sites are using either “Day and Name” or “Month and Name”. Not sure if this is an issue when using site-wide-tags or not…

.htaccess has 644 permissions. Text of .htaccess is below. It contains a fix I got from the referenced wpmututorials URL – that seemed to work for a while (pre-WP3.0) but then the problem started up again after WP 3.0 upgrade.

Thanks!

RewriteEngine On
RewriteBase /

#redirect old site urls to new site
Redirect /ebms http://ednabrewer.net
Redirect /ebmsptsa http://ptsa.ednabrewer.net

#uploaded files
RewriteRule ^(.*/)?files/$ index.php [L]
RewriteCond %{REQUEST_URI} !.*wp-content/plugins.*
RewriteRule ^(.*/)?files/(.*) wp-includes/ms-files.php?file=$2 [L]

# add a trailing slash to /wp-admin
RewriteCond %{REQUEST_URI} ^.*/wp-admin$
RewriteRule ^(.+)$ $1/ [R=301,L]

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

# replaced as per: http://wpmututorials.com/known-issues/rewrites/
#RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-.*) $2 [L]
#RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule ^[_0-9a-zA-Z-]+/(wp-(content|admin|includes).*) $1 [L]
RewriteRule ^[_0-9a-zA-Z-]+/(.*\.php)$ $1 [L]

RewriteRule . index.php [L]

<IfModule mod_security.c>
<Files async-upload.php>
SecFilterEngine Off
SecFilterScanPOST Off
</Files>
</IfModule>