I can confirm this for your OpenOffice.org example in compiz (Desktop
Effects) but not for metacity (without Desktop Effects).
** Also affects: compiz (Ubuntu)
Importance: Undecided
Status: New
** Changed in: compiz (Ubuntu)
Status: New => Confirmed
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when I start GUI app ("p4 diff" for example) from gnome terminal it appers
behind all windows
https://bugs.launchpad.net/bugs/398429
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