This is a bit of a question with some level of detail to it, so let me first explain the situation, then my implementation and last the question so you understand best.
Mmmh, how many points do you have to handle. Can you publish the path, so maybe some other can test it in their own apps. Did you try to reduce the path points with Douglas-Peuker or comparable methods. Did you try other apps like the free "Routeconverter" (which works with HGT) to see if you get better results. Do you need the elevation points direct/on the fly? Would using other free elevation services be an option. Perhaps you have to read the elevation points back to your route points, so that you can sort out unwanted points.
Only some thinking, in bad English - I'm afraid. Good luck, Reinhard