You use your front brake switch whether in neutral or in gear, so that doesn't seem to be it. Have you tried stopping in other gears?
Have you checked the wiring involved in the clutch switch, brake switch, etc.? Trace the lines to make sure you don't have something miswired. Interestingly, in neutral you have the ground shared by all the lights and neutral. In gear, you don't. So it seems there is a circuit shorting out when it doesn't have the transmission in neutral. Just a thought.
Have you checked the wiring involved in the clutch switch, brake switch, etc.? Trace the lines to make sure you don't have something miswired. Interestingly, in neutral you have the ground shared by all the lights and neutral. In gear, you don't. So it seems there is a circuit shorting out when it doesn't have the transmission in neutral. Just a thought.