when this happens, the transparency in quake does not work as it should, You cannot see the windows behind the Guake terminal, It lets you see your Background wallpaper only.
A solution for this is to delay the start up of Guake, so that Gnome is allowed to initialize fully before Guake starts.
To do this , run
under startup-programs edit your entry for Guake.
and add sleep 8 && infront of guake,
sleep 8 && guake
This gives guake an 8 second delay before starting, and should be enough to let Gnome fully initialize, and your transparency will work as it should.