I just noticed that after upgrading SEO Ultimate from 6.5.2 to 6.9.4 the autolinks stopped working on 'included pages' via the plugin Improved Include Page'. No links are created on the lined pages like they were in 6.5.2. When I put the old version of content-autolinks.php back in the autolinks work again but obviously I lost the new function.
I'm guessing that the autolinks are now created before the shortcode is rendered. Anyway to look to see if it can be changed back since I would think other pluggins with shortcode would be affected too?