Hi, sasq.
What version of GlassFish are you using? And what version of Java?
Our goal is for the client to behave the same way, regardless of how it is launched. That takes some work because there are differences in a Java Web Start launch vs. an appclient command launch.
One of the key differences is that in a Java Web Start launch the Swing event dispatcher thread is running before the app client container (ACC) gains control. Because of the way security is implemented on the client side, we have to do some things in a Java Web Start launch to make sure the authentication information is propagated to the EDT. (This happens without any extra work with an appclient command launch because the ACC runs before the EDT starts up.)
In fact there was a bug similar to this that we fixed some time ago, which is why I'm curious about what version of GlassFish you are using that shows this problem.
One other brief question - are you using injection for the remote references or is the client looking up the JNDI names explicitly itself?
-Tim
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