I'd say its right including the times you are not pedaling to calculate average rpm. Your legs are taking a break and it should rightfully be included in the average. If you compare average cadence over the same route then you can make a 1:1 comparision. Actually you can compare average cadence between all trips and it gives you an indicator of how the terrain may differ. Flat route will likely give you higher averages vs. hilly where you may have a slower cadence going up and sometimes zero going down. The botom line is to use average cadence to compare your own rides to each other, not as a comparision to an 'ideal' 95-110 cadence.

If this bothers you then ride a fixed gear bike so you wont get any zero cadence time.

Al