For uploaded Garmin data, only include the actual training time in computing pace/HR averages (not the entire elapsed time)
When the entire elapsed time is counted for workout paces, etc. they are skewed and do not reflect the data in GarminConnect.
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We include zeros in the calculations, but not stop time. This may help.
http://help.trainingpeaks.com/hc/en-us/articles/204070234-Why-is-there-a-difference-in-my-data-between-Garmin-Connect-and-TrainingPeaks-