I'm afraid it's not possible to compare ascent calculations from different sources (maps, GPS devices, other applications) as they all have different methods of calculation. Some people have unerring faith in one particular source and claim that it's the most accurate, but there isn't really a "right" or "wrong". If you want to compare the ascent for different routes you should try to use the same source all the time, as this is the best way to get an accurate comparison. There has been a lot of previous discusison about this on our forums - please see this post and the one it links to if you want to read more about it.
Regarding the sliders on the Route Profile tool, the Elevation Interval slider changes the distance interval between elevation readings, which effectively smooths the profile as you increase the distance, and the Filter Bumps slider removes any short shallow inclines or declines.
I use a couple other apps that also show overall elevation gain in them and I'm getting some wide differences in the totals when I drop the same GPX file into them. The Plotaroute total seems to always be greater. When I'm in the Plotaroute feature showing the more detailed elevation profile, I've noticed the two slider bars on the sides to the profiles. I can adjust these to change the overall elevation gain. Can you give a brief explanation of what each of the bars represents. My assumption is that the other apps have defaults based the same measurements as the slider bars and that they are probably set a a lower accuracy. Would that be correct?
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