i've seen this too. i can tell you a page where it happens often when i try to bring it to the foreground. i click its content and it comes in front of other windows, but isn't active (toolbar still dimmed, omniweb's menues not in menubar)
if i click it a second time, it comes to the foreground.
the site contains 2 frames, one with shockwave content and another with javascript content. (hope that helps)
i was not able to reproduce it right now, but i know it happens frequently.
sadly to enter the site, you have to register. but anyway i give you the link. maybe someone wants to try.
link:
http://www.mohrenbrauerei.at/jassers...php?check=true
another problem on the site is a strange "hanging". the shockwave content often stops responding until i move the mouse cursor. then it continues to work normally.