A chart showing the average fps should be showing an average of *all* of the fps measurements taken throughout a given run. For example, if you have a 2 minute run you are doing, and your measurement tool samples the fps every second, then you'll have a total of 120 measurements taken during the run. An "average" should be the average of *all* of those 120 measurements. For consistency, it's best to do a run about 3 times, then average together those three averages.
I might be misunderstanding your question, though...