Is it really identical (the same activity) just with a changed activity type? The length differs, so it is already strange, if it is really the same activity. Are the HR profiles identical in both cases? The best would be tapping the share symbol at both activities and posting the links here, so that we can look at the details.
Manual activity cannot have the same Calories expenditure as a recorded one, because it does not contain the HR data that a recorded activity has. And since Calories are derived from the HR data, Calories differ each time even if you use the same type of activity.