Hi John,
Your response calculation technique looks sound, otherwise you would note get a good match when applied to the reference measurement. It does seem though that something must have changed between the observations. There are a few things to check
I ran into a similar problem when I first attempted this type of exercise soon after I got the ALPY. In this case it was due to a combination of chromatic aberration and a shift in focus. I have attached the details.
Combinations of chromatic aberration, atmospheric dispersion, focus and the position of the star on the slit can all conspire to give these sort of problems. Christian Buil has a particularly scary page on the problem somewhere. I will see if I can dig it out. Having said that your C6 without focal reducer I would guess does not suffer from too much CA.
Other things to watch in processing is to make sure your binning zone includes all the spectrum and the background zones are free from any spectrum data. If you use the optimised binning in ISIS try switching it off as I found the similar feature in VSpec could distort the spectrum under some circumstances.
Cheers
Robin
EDIT: here is the link I was looking for