I also experience this problem, but I only when an instrument approach is added to a flight plan. If the planned flight does not incorporate an instrument approach Plan-G will continue to display the black track line, and I can display and view instrument approaches as normal, but if I try to actually add one to my plan the the track line for the whole of the rest of the flight disappears, leaving only the waypoints and the instrument approach visible. If the instrument approach is cleared from the flight plan, the track line reappears.

I have tried turning Map Overlays on and off again but this didn't seem to help. I'm running Plan-G v3.1.1.94 under 64-bit Windows 7.