Starting programs like Emacs frustrates me, because they start by default on the top of my screen. My panel is also located on top and I usually cannot reach the programs title bar to replace it so I have to move the panel, grab the program and remove the panel.
Additional information: Ive setup Desktop margin top to 45, all programs wich remember their position wont pop up under my panel because the desktop is limited to screen - 45. But programs who dont recognize this feature wont obey to your tweaks. For instance Emacs.
The problem is that emacs does not obey to the standards defined at freedesktop.org. We can't do much about it .. but as a fix you might want to autohide the panel.
Alright, closing this since it is not a bug. Please keep in touch through the mailinglist. Thank you.