It’s normal. myGeonaute recalculates the height difference using your GPS tracking coupled with a cartographic database. The result is therefore more accurate than with your product.
We’ve chosen to do this as GPS technology allows for accurate longitudinal/latitudinal positioning, but doesn’t allow for altitude to be measured accurately. It’s therefore more efficient to deduce the altitude at each point by using the longitudinal and latitudinal data coupled to a cartographical database which gives use the altitude.