There is a minor bug that occur only when SEO clean URLs are enabled in x-cart AND you have Ability template's "Redirect old IE browsers to browser upgrade page" enabled.
This causes a 404 error when the browser tries to go to a category .e.g
www.xyz.com/My-Category/ as it tries to redirect via JS to "upgrade.html", which in this case means it tries to go to
www.xyz.com/My-Category/upgrade.html instead of
www.xyz.com/upgrade.html.
All I did to fix this was to add / in in front of /upgrade.html in /skin/ability/custom/common.tpl on line 99 so it looks like this:
<script type="text/javascript"> window.location="/upgrade.html"; </script>
Please note I found this to be a problem when using Google Adwords as the resulting 404 error was causing the ads submitted with clean URLs to fail but would work fine without them be cause the path was valid as it was in the root URL.
It is an odd combination but it can be a huge pain in the lower back if you are using Adwords.