EXECUTE: Create JSF Kickstart project. (e.g. JSF 1.1 with libs)
EXECUTE: Open web projects view.
ASSERT: There is the created project.
EXECUTE: Open .projects
ASSERT: There is jboss tools JSF nature.
EXECUTE: close and re-open the project
EXECUTE: Open web projects view.
FAILURE: There is not the project.
EXECUTE: Open .projects
FAILURE: There is not JSF nature.

If you can't reproduce it just close/reopen it a few times.

I can reproduce it in 2.1.1GA and 3.0 (trunk).