Inconsistent Broken Permalinks

I am running into an odd issue. For the majority of posts on my site, clicking on the permalink from the category archive page results in a an error message (“Sorry, no posts matched your criteria.”) unless the item happens to be linked to from the front page of my site.
My permalink structure is really basic:
/archives/%postname%/
Resulting in this .htaccess:
RewriteEngine On
RewriteBase /
RewriteRule ^archives/category/(.*)/(feed|rdf|rss|rss2|atom)/?$ /wp-feed.php?category_name=$1&feed=$2 [QSA]
RewriteRule ^archives/category/?(.*) /index.php?category_name=$1 [QSA]
RewriteRule ^archives/author/(.*)/(feed|rdf|rss|rss2|atom)/?$ /wp-feed.php?author_name=$1&feed=$2 [QSA]
RewriteRule ^archives/author/?(.*) /index.php?author_name=$1 [QSA]
RewriteRule ^archives/?(.*) /index.php?name=$1 [QSA]
RewriteRule ^archives/([_0-9a-z-]+)?/?([0-9]+)?/?$ /index.php?name=$1&page=$2 [QSA]
RewriteRule ^archives/([_0-9a-z-]+)/(feed|rdf|rss|rss2|atom)/?$ /wp-feed.php?name=$1&feed=$2 [QSA]
RewriteRule ^archives/([_0-9a-z-]+)/trackback/?$ /wp-trackback.php?name=$1 [QSA]
RewriteRule ^feed/?([_0-9a-z-]+)?/?$ /wp-feed.php?feed=$1 [QSA]
RewriteRule ^comments/feed/?([_0-9a-z-]+)?/?$ /wp-feed.php?feed=$1&withcomments=1 [QSA]
The most confusing aspect is the fact that some work and some do not. I have looked at the structure of the permalinks on both sets of pages and cannot see any difference in them.
All of the links on my main page work properly. If you visit a category page Cooking for example) you can click on the first permalink (“Mmmma€| Summer Drinks”) and it will work because it also happens to be on the main page. But the second link (“The Thermochemical Joy of Cooking”) does not work as it is not on the main page.
I am running 1.2 with the following plugins activated: Search Hilite, MarkDown, Syntax Highlighter 2, WP Style Switcher.
Any help would be truly appreciated!
Alex