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I’m having very similar issues to what is described in Pagination wonkiness. I have index.php from the General Configuration path settings, and am using the LG .htaccess Generator extension to remove index.php from the path. Everything is working fine except for pagination.

If I am on the “home” page the following does not work:
- http://domain.com/, click a pagination link to http://domain.com/P1/, returns a 404.

However this works correctly:
- http://domain.com/site/, click a pagination link to http://domain.com/site/P1/, returns page 2.

The post above suggested using the replace plugin to add the template group back into pagination links, but i’d like to know if there is a way to achieve this with .htaccess instead, in such a way that pagination will work whether you are on the home page or the template group page.

I was able to add some code to my htaccess file to redirect visits to the site root to the proper template group. This seems to do the trick so for now, that’s what I’ll use. If there is a better way let me know!

RewriteCond %{REQUEST_URI} ^/$
RewriteRule $ http://%{HTTP_HOST}/site [L,R=301]

Glad to see you found a solution. Please post again as needed.