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I've set my panels to auto-hide and want them to be on top of everything once they scroll out.
Which gconf-key do I have to use to achieve this?
Also I looked for a list of gconf keys -- somebody knows?
What you're seeing is a bug. It occurs on my system (11.04) from time to time but I can't properly reproduce it and don't have a reliable fix either. It's not a simple gconf setting. There are various workarounds on the ubuntu forums you can try.
I think you're looking for:
ALT-F2 > "gconf-editor" > apps > panel > toplevels > top_panel_screen0 > auto_hide_size > 1
Required, but never shown