I just updated the plugin to v.126.96.36.199 and have an issue that didn't occur before (to my knowledge).
The menus on my WP site at http://explosiveoptions.net and two other sites where the plugin was installed had their menubars messed up.
The menus had categories as their primary items, and usually go to category archive pages when clicked.
Now, with the plugin active, the menus don't go to the category archive page, they either 404 or dynamically go to a random post with that menu item's term in the URL.
I've had to deactivate the plugin to prevent this from continuing to occur, but have confirmed no other plugin is causing this issue.