Hi folks! I've figured that we blow up pretty nasty when using latest MyFaces on Tomcat with any CDI container (OWB or Weld). That's because you must not use BeanManager#getBeans before AfterDeplyomentValidation gets fired.
I think the whole handling should ONLY be done via a CDI Extension! In which way it will automatically get picked up and will initialise Flows perfectly fine. The only problem to solve is how to make the FacesContext available from within the CDI Extension. The ticket is tracked as MYFACES-4224. Feedback welcome. LieGrue, strub