The version of NHibernate.Linq that is in the main trunk is the active version and the one that will be supported in the future. The version that is in Contrib has some limitations in it that forced the team to go with a new approach. NHibernate 2.1 will come out with official Linq support.
However if you are looking to use Linq with NHibernate 2.0.1GA then you can go here
http://slagd.com/ for the contrib version that has been patched to work with 2.0.1GA. However this version will have some limitiations.