Audacious (and XMMS) use a similar "window style". They create one or more windows without the standard window decorations. A bug in the xfce4-panel's Task List prevents it from minimizing (and unminimizing) Audacious when two windows are displayed on the screen. For example, if both the main window and the playlists window are displayed, the Task List will not be able to (un)minimize those windows. Other task lists in other panel (lxpanel, gnome-panel) can properly unminimize both Audacious windows together. With xfce4-panel, sometimes the windows will minimize, but they will never unminimize. To unminimize I have to switch to a different virtual desktop and then click on Audacious in the Task list (surprisingly, it is still listed, even though I have switched to another virtual desktop). If I close the playlists window, so that only a single Audacious window is visible, xfce4-panel and (un)minimize that single window correctly. I tested this with both Openbox and Gnome. The problem definitely seems to be xfce4-panel. This problem should be easy to reproduce on any system with Audacious. Old versions of xfce4-panel did not have this problem. This problem appeared when I switched from Ubuntu 8.04 to 10.04.
It seems very unlikely this works in gnome-panel but not in xfce4-panel 4.6.x, because both use the same code (libwnck). Is this with the same window manager (xfwm4)?
Looks like I was wrong. I can now only reproduce the problem with xfce4-panel + openbox. xfce4-panel + gnome (is metacity Gnome/Ubuntu's window manager?) seems to work fine. gnome-panel + openbox works fine. (Openbox is a window manager.) I'll test further and report back. I don't use xfwm4, and therefore have not tested with it.
I compiled an old version of Openbox (version 3.4.6.1) from source code. The problem went away. So it would seem that it is a problem with Openbox. It is interesting that the problem only appears with xfce4-panel, and not with other panels. I am changing this bugs status to resolved/invalid.