Could it be that these flickering lights are at the edge of your draw distance? Next time it happens, face the suspect lights and walk backwards (away from lights). If they go dark immediately, this is probably the case. ESC->Options ->Video has a few settings that might affect this, most notably View Distance.
Could also be a Dynamic Mesh/phantom block TnL issue - hit F1 to open command prompt, then type "pois" (without quotes) and hit enter to toggle on/off. Haven't experienced this one since last major alpha and a major hardware upgrade, so might've already been fixed.