I would guess that CMake has a more intelligent macro to get the X11 directory and that the current set of Makefiles have fallen behind this.  I should probably look at using CMake in the near future for the G4 build, but it is a major reengineering of the Geant4 portion of SimDist.  Perhaps you can find where this is hard-coded in the Makefiles and change it manually?  Not sure...

You may also turn off visualization entirely, which I realize is not a long-term solution but may at least get you a working batch build.

I'll look into it further and let you know.

--Jeremy