After I run the pcb-gcode script in Eagle and the bottom layer is generated and the drilling is generated I am not sure about this: Do I need to flip the pcb to drill it? Because if I deselect the "Generate top drills" and leave only "Generate bottom drills" there is no output file for drilling. I am confused.
That's strange. I just re-checked it here and it works fine. Is there something off with your layout? Maybe just try a board with some vias on it.
I'm using Eagle 5.3.0