I haven't looked into this extensively, but since the WP 3.5 update Vimeography has stopped working and causes all sorts of issues.
One of the first I noticed was that it blocked the WP Plugin Search from connecting to WordPress. It also broke other apps that are running on Jquery.
My theory is that there is something to do with the way the new WP handles Jquery vs. the way it used to.
This is also possibly a theme conflict, but I haven't had a chance to test this theory yet.
Loved this plugin - hope the next update fixes the conflicts!!!