The reason is because before homing the machine, the kinimatics are stuck in "Joint" mode, and the gui buttons for jogging the Y axis are only connected to joint#2 (the normal Y joint). And this is why jogging is usually disabled before homing in most gantry configs in Linuxcnc. I have not played with this my self, since I don't have any gantry machines currently set up for Linuxcnc.
I've wondered if there might be a way to tie both of the Y-axis' joints jog command inputs together before homing so that they could be jogged. I'm pretty sure it could be done without too much trouble using external inputs from physical jog buttons or MPG, not so sure if the jog buttons in the gui screen could be made to work though since their signals don't go through hal. I can't say that I've seen any examples of how to do this posted anywhere, but I haven't paid real close attention to the subject. I suspect most people just accept that you can't jog the gantry before it is homed.
