Internet Explorer Java app problem when ESSO client runs on machine

Hi,
I face following situation:
User is working with web application. It is a kind of interface for Document Management System. This application logon is not managed by Oracle Enterprise SSO client (or agent).
When an Oracle ESSO services run on user's computer, user cannot open PDF files from DMS Internet Explorer page with error: UNABLE TO DOWNLOAD APPLET DUE TO SECURITY ISSUE.
When an Oracle ESSO services do not run on user's computer, user can always open PDF files from DMS Internet Explorer page with no errors.
I checked the Internet Explorer security settings and there I can see no limitations on Java, scripts or ActiveX.
My question is:
how Oracle ESSO client/agent affects other Java-based applications or applets?
is there any possible reason while Oracle ESSO client is installed to user computer with package including "Java helper" item?
is there any known and described issue within?
Thank you very much for any answer.
Regards, Kamil
Message was edited by: KamilBrzak
Addition: Described behaviour was under IE8 and IE9. Firefox 22.0 and IE10 works correctly. Java version is 6.21. Operation system is Windows 7 x64.

Say your stub is in a jar called stub.jar.
You need to put that stub somewhere that it can be reached through a protocol for which Java has a URL type - so you can put it on a shared file system and use a file URL or behind an http server and use an http URL.
Let's use http - put stub.jar at the docroot of a web server.
Then, when you start your SERVER code, include this VM parameter:
-Djava.rmi.server.codebase="http://<serveraddress>stub.jar"
Now your client will be able to use http to load the stub file out of stub.jar through http.
If you do use a file URL, make sure the shared directory you put your jar in is not on the client's classpath.

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