In the basejpi.htm there is the applet parameter applet_stop_timeout which is default set to 500 or something. Try increasing it (maximum is 3000). The parameter basically sets the time which the applet has to destroy itself gracefully after the browser is closed; I guess if the forms applet does not have the time to destroy itself gracefully it hangs causing the java process not being able to close.
Thank you!!! Bumping it to 3000 fixed my problem. java.exe closes normally now.