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When you open a pop-up decoration, besides its being badly positioned (issue 126932) it is not scrolled with the rest of the diagram. I'm attaching a video illustrating the behavior. Sorry for the format, it's Quicktime.
Created attachment 56727 [details] Screen-capture
I cant check the screencap video you provided (because .mov format is a proprietary thing for this weird :D mac platform) but based on description, i can say this bug is fixed.
* http://www.apple.com/quicktime/download/ * http://www.codecguide.com/download_qt.htm ;)
Tested and verified using NetBeans IDE 6.1 (Build 200810140114) and no pop up occurs on top of scroll bars.