Cannot work with two Swing app. at the same time.

Hi guys,
I bring this problem here may somebody experienced that.
I developed two client side applications(applets). Locate them 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/her PC and ready to work. (In index.html I used JavaScript function 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 little 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?
Note that the two app. have no Communication with each other.
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.

I am also facing the same problem !
Since this may be a very late reply , if any body has a solution pls share!
What I understand is that when we use javascript:window.open() it opens a new browser window
but under same JVM. This is helpful if we need to have a 'Close window' button/link in the newly opened window and use javascript:window.close() there. Then browser will not show us the confirmation dialog box 'Webpage you are viewing is trying to close the window. Do you wish to Proceed?'
But if we want a new JVM for each opened link and also donot want the popup dialog to be displayed when we close the browser from there..what do we do??

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