I found a band-aid that will bring back functionality of the navigation menus, however it may bug something else out. As it’s been a year since the developer has updated this plugin, I would take it as such that there will be no other fix anytime soon.
http://wordpress.org/support/topic/breaks-sub-menu-items-on-bootstrap-theme?replies=2#post-4318466
figured out what code was breaking it. not really entirely sure of what the class did in all honesty. I’m sure it was something important at one time, but as far as I can tell it fixed what I need this plugin for.
I just commented out lines 38-112 of wordpress-access-control.php
you can find it here, http://pastebin.com/3AMHGekh
like i said, this works for me. take it as a band-aid approach, i’m sure this will take some type of functionality away from the full plugin. make sure you backup your original, or just remove the comments from this one.