FULL PRODUCT VERSION :
JDK 6u95 b12

ADDITIONAL OS VERSION INFORMATION :
MS Windows 7 OS

A DESCRIPTION OF THE PROBLEM :
When an applet loaded in Internet Explorer (IE) 9 with Classic Java Plugin from JRE 6 shows "javax.swing.JFrame" instance on which the method "java.awt.Window.setAlwaysOnTop" was called, the shown frame window is positioned correctly on top of all windows on the desktop. However, after the applet shows JavaScript "alert" modal dialog via LiveConnect call and after the applet shows Java modal dialog, for which the frame is specified as a parent, from a parallel thread, then after closing of the described two modal dialogs, IE 9 window can be put on top of JFrame instance. This result is incorrect from the view point of the user, since "java.awt.Window.setAlwaysOnTop" method was called on the instance of JFrame.

WORKAROUNDS :
Load the applet with next-generation Java Plug-in, however the user cannot use this workaround.