Right clicking on a panel item and choosing "customize panel" leads to an always on top window appearing. Also launcher properties have this effect as does the property window for the shutdown buttons (I guess it's anything internal to the panel). The external plugins that are in the panel don't generate always on top property windows so this is inconsistent. According to one Debian user it's a "bad for usability and user interaction". I'm not hugely convinced by that argument (why would you want the customize the panel window open long term?) but I thought you might like to know about this bug. The Debian bug is at: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=372824 Thanks.
This is probably a side effect of the panel being a docktype window. The dialog is probably placed at the same layer as the panel, i.e. on top. External plugins are separate processes, which is probably why they are not recognized as being part of the panel. I would worry more about the inconsistency than the fact that it is always on top. I probably won't have time to look at this soon, and it is not a very high priority for me. Thanks for the report.
Ok, should be fixed in the next beta release (or SVN revision 22740). Thanks.