Comment 14 for bug 155101

I still experience this in Maverick, with applications which can be minimized to tray, such as Pidgin and Gwibber. I've struggled with more show-stopping display bugs, so I haven't really followed if this particular behaviour has remained unchanged through 8.xx and 9.xx versions.

Unlike described in earlier comments, in my case the affected windows move upwards and and a little to the left with each reopening, eventually causing the titlebar to end up behind the top panel. If one keeps clicking the tray icon to close and reopen the window, eventually Compiz (or whatever causes this) seems to realize its mistake and pops the window back below the panel instead of behind it.

Apparently the time between closing and reopening matters; If the closing animation is still running when the window is reopened, the positioning always goes wrong.