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I have a dual-monitor system with Debian Linux using the NVIDIA-Linux-x86-100.14.11 driver with Xinerama in KDE. If I maximize the main NetBeans window (NetBeans 6.0 Milestone 10) so that it is full-sized on one monitor and I click on and drag a tab for a file that is open in the editor to my other monitor, the window that is created flickers and/or appears to momentarily resize itself to the height of the screen. If I move the main NetBeans window over to my other monitor and repeat this process the window does not flicker, but it instead moves very slowly when being dragged. Moving the maximized main window so that it is mostly off-screen results in the same behavior. Reducing the width and height of the main window seems to prevent this behavior, although dragging the window is very slow. Subsequent drags of the window do result in any problems after the mouse button is released after initially clicking on and dragging the editor tab. Clicking on and dragging a window (e.g. Projects or Files) does not result in any problems. These problems do not occur in Windows XP on the same computer.
I tried NetBeans 6.0 in the Gnome desktop on a notebook computer running Fedora with a single monitor and a Radeon video card, and the same problems occur.
I can reproduce on my Ubuntu 7.04 Linux, gnome, either beryl or metacity WM. Reproduction case is somewhat different then yours, but the symptoms are the same - flickering and slowness.
fixed in main trunk: Checking in WindowDnDManager.java; /cvs/core/windows/src/org/netbeans/core/windows/view/dnd/WindowDnDManager.java,v <-- WindowDnDManager.java new revision: 1.27; previous revision: 1.26