Ok, so let me just make sure I understand what you're doing.

Yo have a JSP that binds some object to JNDI by doing something like:

  | ...
  | InitialContext context = new InitialContext();
  | context.rebind("myObject", myObject);
  | ...
  | 
Then, in your EJB, you are looking up this object, with something like:

  | ...
  | InitialContext context = new InitialContext();
  | MyClass myObject = (MyClass)context.lookup("myObject");
  | ...
  | 
Some things to try:
1) Pass myObject as an argument into the EJB's business method.  This would 
work if the JSP is invoking a method directly on the EJB during the same 
request.
2) If instead you are calling a JSP to bind this object, then making a separate 
request to invoke the EJB that uses the bound object, then try storing your 
object in the HttpSession in the first JSP, look it up in the session from the 
second JSP, and then pass it to the EJB during the business method invocation.
3) Create a jndi.properties and put it in the root of your EAR. Your EJB should 
prefer that jndi.properties over the system jndi.properties.

It sounds like your using JNDI as a way to pass arguments from your JSP to your 
EJB.  I'm sure you have a good reason for doing this, but if I were you, I 
would redesign the JSPs/EJBs to use a more conventional means of passing 
arguments (i.e. suggestion 1 or 2).

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