Hi Bryan,
I'm not exactly having the same issue, but closely related. When I'm in the 2D panel state, when doing the Before start Checklist the FO will put the Beacon on as per normal. But when using the VC panel state. The FO will toogle the NAV light off and the Beacon will remain in the off position. I'm suspecting that in the VC when the mini panel appear, the simulated mouse click toggles the wrong switch. Don't understand really why.
Fred