I have the same problem. I'm trying to upgrade from 4.0.1sp1 to 4.0.2. Does anybody know the answer?
The reason the error message says 'GEN-SiteEJB' not found and not 'local/GEN-SiteEJB' is because it has been able to find the local context it just can't find the GEN-SiteEJB under the local context.
Regarding accessing the local home see: -