Or maybe you are experiencing typical Strat hum. Single coils will buzz/hum. That's why humbuckers were made, to stop that. If this is the case then your Strat should get that noise if the pickup selector is i positions 1, 3 and 5 (selecting the individual pickups). In positions 2 and 4, since it is selecting 2 pickups at once it acts as a humbucker.

If that isn't the issue then I'm not sure. Does it ONLY make noise in ONE position and clean an all the others?