A couple of times, I have set up a flight and simply selected "Active Runway." However, clicking "Fly" the program positions me on the wrong runway.Why does this happen and can it be avoided? The whole point of selecting "Active Runway" is if I am wanting to save time.

Active Runway means the runway being used for the prevailing weather conditions based on what MS thinks it is (which may or may not be correct).For example, for KBFI, if the wind is calm, it'll position the aircraft at 31L, which is the "calm wind" runway.