I use EJB 3...Is there any good reason to use a EntityManager with:

@PersistenceContext
EntityManager em;

instead of SEAM managed persistence context:

@In
EntityManager em;

In both, you can set FlushModeTypes and force atomit transactions.

When should I disable Seam-managed transactions/EJBTransaction???

I have red chapter 9 of the SEAM-Reference but it was not so clear, when to decide to use the one or the other in an EJB-Project.

Seam transaction management is useful even if you're using EJB 3.0 container-managed persistence contexts.

Why?
Because of LazyInitializationException or NonUniqueObjectException?

Any Best Practice?