Did you try looking up java:module/MyEJB within the webapp? It should work.
The reason the module-scoped jndi name is not logged is, it's only scoped to
the module and not exposed to other apps in the server, whereas the global
jndi names are accessible to all deployed apps. For the same reason, any
java:comp/**/* or java:app/**/* jndi names are not logged either.
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