I see cropping the spectrum to remove the bad edges is mentioned in the ISIS tutorial ~ 2/3 the way down. I think you have just missed that step
“Tip: The response profile changes shape very rapidly near the edges and it may not accurately represent the response in these regions as the signal there is almost zero. It is a good idea to crop the useful part before smoothing the spectrum. Use the “Cut” tool for this operation. The smoothing will then be easier and the results better. Here is the smoothing result under these conditions:”
Cheers
Robin