I suspect this is the menu bar. Current code tries to hide it by
forcing the widget size to 0x0. In gtk2 this results in a small white
line at the top of the screen, probably because the minimum widget size
in gtk is 1x1. In gtk3 this doesn't work at all and the menu bar
remains visible. This isn't a new issue btw.
I've tried to fix that with a simple gtk_widget_hide(menu_bar) call.
Which has the side effect to also turn off all menu accelerators. Which
is a non-starter, especially for Ctrl-Alt-F not working any more.