I saw this kind of exceptions for example when the client and server version do not match, i.e. when an "older" appclient is trying to access a "newer" EJB server. In GFv2 we also had inconsitent state when restarting the domain, so now we always undeploy, stop-domain, start-domain and then deploy our app.
But I remember there were also some problems with IIOP in different JVM versions. We once downgraded all our clients to sun-jre-1.6.0_02 because the newer releases also caused weird IIOP exceptions. It seems to me that IIOP clients are not very well supported in glassfish. Everyone is talking only about web applications and SOAP services these days.
The problem was so annoying that in the end we decided to throw our whole appclient away and rebuild it as a web application. Maybe you also want to consider using SOAP instead of IIOP as the client-server protocol.
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