I suspect the system has a barometric altimeter somewhere because it makes different mistakes than a GPS elevation output. There is an option in mission control (I can't see it now, so probably under "tune") to "sync elevation with GPS". Do you have that on or off?
Also if you have existing .fit routes with only position data, there are tools that will import them and apply elevation from DEM data. You might want to see if the tools you like to use have that option.