Set the panel to be transparent, turn on "Make active panel opaque" and log out and in again. The panel will be opaque even though it is inactive, and will become transparent if the mouse cursor is moved over and off it again.
Can't reproduce this. Are you using the Xfce window manager? Maybe that is started after the panel.
Yes, using xfwm4.
Never seen this problem myself. Once the devel panel lands in trunk i will close this since the new code handles this differently.
Devel branch has been merged in master. A 4.7.0 release will follow soon. If you think this bug is not fixed? Feel free to reopen the bug.