Hey tallmanproductions,
The user here: http://wordpress.org/support/topic/staff-1?replies=5 had the same issue. My experience with MU is really limited. As I understand it, its a problem with the way options are handled in the MU environment.
This is a really long-hackish work-around (but I've not tested this) and I apologize in advance:
You may try opening up admin-views.php as well as admin-install-uninstall.php and replace every instance of 'update_option,' 'get_option,' and 'delete_option' with 'update_site_option,' get_site_option,' and 'delete_site_option' respectively. You may also need to copy the plugin files down to a local drive, then uninstall and delete the plugin via the WP admin. Then copy the plugin back up to the server and re-install.
This should make sure that any stray options get deleted from the options table and the new options get added to the correct options table on the new install.
Again, I haven't tested this but it sounds like it might work in my head. Haha.
Let me know if this helps and I'll start thinking of a way to incorporate MU support in the next version.
Thanks!
Brett