The problem is that in /usr/share/X11/xkb/symbols/pc/ there is no file named el but the is one with the name gr. Unfortunately the x server tries to open pc/el and not pc/gr and as a result the greek layout gets omitted. A simple fix is to have a link in that folder from el to gr. That fixes the problem for now. I have posted this bug in xorg's bugzilla https://bugs.freedesktop.org/show_bug.cgi?id=5012 and I'm waiting for an action from them. I just wanted to inform you about that in case someone wants to try the new xorg and uses a greek layout.
Thanks, I'll indicate to track it there.