New browser window to be shown on top of the applet's window instead of the original browser window.
Will see that new browser window opened on top of calling browser window but beyond the separate frame window.

When you uncheck "Enable the next-generation Java Plug-in" this flag from control panel, you will see correct behavior.

See note for problem reproductions steps.
Repro test case is attached
Steps to reproduce:

ShowDocument.class*
ShowDocument.java*
applet.htm*

1) Copy class and html file in same folder
2) Launch html file
3) This will launch separate frame
4) Click on Go field

Will see that new browser window opened on top of calling browser window but beyond the separate frame window.

When you uncheck "Enable the next-generation Java Plug-in" this flag from control panel, you will see correct behavior.

** NOTE **
the cusotmer has also provided a video file demonstrating the issue
Probl1.zip
I have provded a copy of 1.6.0_18 provided by Calvin Cheung
and it did not resolve this issue.