I've just had a look at the PMDX manual, it looks like you should be using pin 14 or 16 of J8 and JP3 should be set to 'outputs enabled', that's what it looks like after a quick read anyway. The outputs have an LED so it should be easy to see the state of your chosen output. I can't see the ESS making any difference so I would disconnect the flasher and concentrate on getting your bob output to go on and off from the software and not using the Brain function. When you get the output to operate correctly then connect the flasher and it should go on and off with the output. Now bring the Brain into operation and provided the logic is okay the flasher should operate.
It may be that the lamp is dim because it's being switched at high speed, try a multimeter with frequency range across the lamp.