Reproduce steps:
1. RDP to the machine below
Maincesc22bk04.us.oracle.com (winxp-pro-x64)
user: uadmin
pass: changeme
There is already 64 bit b-40 installed on this box

2. Access http://sqeweb.us.oracle.com/deployment1/deployment_6_UR_int_exec_ws/6/deployment/src/javafx/fxfeaturesTest/fxfeaturesTest/html/FullscreenTest.html in IE. Click on "Toogle Fullscreen" of the stage inside the browser. Then the stage inside fx applet will become totally transparent (or invisible?) There's no effect of any key inputs or mouse click. Only pressing ESC could make the stage back to normal size from full screen mode.

3. If you can see the above symptom, then the issue is reproduced. (I left the IE open on this machine, anybody can simply login to it to see this issue.)

NOTE:
1. The "second stage" works fine.
2. javaws works fine. (Try javaws http://sqeweb.us.oracle.com/deployment1/deployment_6_UR_int_exec_ws/6/deployment/src/javafx/fxfeaturesTest/fxfeaturesTest/html/FullscreenTest.jnlp)
3. x86 box works fine.