Hi Ben
Does your site come up without SEO on? Does it work if you're not using anything SEO and rename the .htaccess file back to htaccess.txt?
YES......
If I use this .htaccess
## Can be commented out if causes errors, see notes above.
# Options +FollowSymLinks
RewriteOptions inherit
RewriteEngine On
RewriteBase /bin-cgi/
RewriteRule ^.cgi$ - [T=application/x-httpd-cgi]
RewriteCond %{REQUEST_URI} (/|\.htm|\.php|\.html|/[^.]*)$ [NC]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
# RewriteRule (.*) index.php
with all SEF REWRITE & Suffix enabled I get a 404 error on any links, if only rewrite & SEF enabled links return 404, if rewrite disabled I get all but with the index.php added to url /index.php/directory-search and images tend to return a red X ... I am of a mind to give up with this... Being attemting to get this right since April..