Hi - Just upgraded to WP 3.1.1. and to Tiny MCE Advanced Version 126.96.36.199. When the plugin is activated, WP's internal linking does not work.
In the plugin settings, none of the Advanced Options were checked. Just for testing, I checked the Advanced Link option, but internal linking still not working.
Not sure if anyone else is reporting same issue? Right now I've deactivated the plugin and WP's internal linking is functioning again.