ibstmt,
Can you please clarify whether you have installed JPA facet to the EJB project ? If not, you need to install the JPA facet to EJB project (by right clicking on the EJB project and then select MyEclipse > Project Facets [capabilities] > Install JPA facet) to show the EJB project in the browse window of the EJB3 reverse engineering setup.
For more information on EJB3 reverse engineering in MyEclipse, please follow this tutorial.
Hope this helps and let us know how it works for you.