I have Ubuntu 12.04 x64 running Unity3d. I downloaded Eclipse from eclipse.org (not the software center) and created a desktop using gnome-desktop-item-edit. The resulting file is below, and I added it to the launcher on the left of the screen by dragging that file on.

#!/usr/bin/env xdg-open

[Desktop Entry]
Version=1.0
Type=Application
Terminal=false
Icon[en_US]=/home/kevin/eclipse/icon.xpm
Name[en_US]=Eclipse
Exec=/home/kevin/eclipse/eclipse
Name=Eclipse
Icon=/home/kevin/eclipse/icon.xpm#!/usr/bin/env xdg-open

However, when I minimize eclipse, eclipse disappears. There is no arrow to the left of the icon in the launcher like usual. And when I click on the launcher again, it tries to relaunch eclipse instead of bringing back the one that was minimized. Eclipse also does not show up when I alt-tab.

I know it is still running because I can see it running with the system monitor.

Note that Eclipse works properly until it is minimized. I have observed this behavior on two different computers now. Does anyone know how to fix it?