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Did you migrate all you application to EJB 3.1 already or are you testing the old application as is?
I would suggest deploying a simple (one EJB) application that is built with EJB 3.1 in mind from scratch and making sure the deployments both for client and server work as expected first.
From there you could them migrate the application 'module by module' so that it is easier to pinpoint the source of errors.
I could build a very simple EJB app and deploy, but I can't migrate the application module by module because there are libraries and code from each module that are co-dependent. I would have to comment out hundreds of lines in a ton of files to get rid of all of the dependencies...I'd like to avoid doing this. Is there a better way to migrate module by module that I don't know about (the above method is all i know).
My current running theory is an issue with libraries and their locations, but I don't know how I could change things without rewriting the entire application. Thanks for your help!