Yes you can have this problem if the nut is loose but you could see what happens if you take off the rubber boot, maybe even the rubber mat/carpet, so that you can see the gearstick coming through the floor. You might have soft engine mounts or gearbox mount rubbers which allows the stick to hit the edge of the hole. A tight fitting boot can also put pressure on the stick. Fitting heavy non standard gear knobs can also cause this problem as they give more leverage when the car hits a bump. The change should be light and sweet even when the engine isn't running.