Using the plugin API, I have found two errors.
1) p2p_is_connected - This returns true if the first parameter is connected to anything, regardless whether it is connected to the second parameter.
2) p2p_connect - I am connecting two custom post types, but the reciprocal argument isn't working in the ui. If I call it as p2p_connect( cpt1, cpt2 ), it doesn't show up in the UI, though it is stored correctly and returned correctly using query_posts. If I reverse the arguments however and call p2p_connect( cpt2, cpt1 ), it does show up in the UI.
Thanks for a great plugin!