Cannot work with two client side applications at the same time!!

Hi guys,
I developed two client side applications(applets). Locate the on Apache/Tomcat. There is also a Index.html file with two links, so when user clicks on each link the associated application will downloaded on his PC and ready to work. (In index.html I used window.open(�) to load the applications)
Now please see this scenario:
1-I ran/loaded both application in two separate browsers(IE5.5). And tried to work with them(minimized one and work with another). Soon I faced unexpected frizzing/locking or very slow running on both applications.
2-Then closed/killed one of them(killed IE). Then re-executed same application again. The application loaded with the last activated screen . Seems it never killed and it was still alive.
3- The only way to successfully working is one by one.
means execute & work with one, then kill that, and then execute and work with another.
To Debug:
When both applications were running(each on it�s own IE), I opened the Task Manager and saw there was only one IEXPLORER.EXE was running, also there was only one Java VM (a small bird icon) on right-bottom of the screen.
I believe this causes the problem. seems they both running in the same session. Since I opened two applications in two IE I was expected to see two IEXPLORER.EXE with two JVM. Am I right? Do you think so?
Any way, Now I am seeking to find the solution. My primary mind says probably I should not use window.open(..) in index.html to load the applications.
Would appreciate any command on this.

Cross post
http://forum.java.sun.com/thread.jsp?thread=184829&forum=31&message=589933

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