I’ve experienced the same problem as John with the same sequence of Miles spectra which Robin used. The response profiles calculated for each star give an excellent match with the Miles spectrum for that star but differ from star to star. All the spectra were taken over a period of an hour at an air mass of around 1.2 with no change to the equipment including focus and no obvious change in atmospheric conditions. However, I do live about 50 miles west of Heathrow and planes are flying over at high altitude all the time. I recently asked on the ARAS Forum if anyone have noticed changes in atmospheric response due to aircraft con trails but so far there has been no response. Possibly a bit of a long shot.
I repeated the exercise a few days later and found the same variation, again different response profiles from star to star but no consistency with the first set. I now plan to experiment with varying the position of the guide star relative to the slit for the same star to see what effect this has. That will not be for a while as the forecast here is bad for several days.
I’m using a LISA with a 23 micron slit on a C11 with a focal reducer operating at f/5.5. The slit size on the sky is 3.1″ which is a reasonable match to the seeing here. These is a noticeable fishtail on the spectra due to a combination of chromatic aberration in the LISA and the FR lens but I include the full fishtail that in the binning zone and do this with the same binning zone for all the stars. I use the optimal binning option in ISIS but switching that off has no effect on the derived response profiles. It is not a problem with smoothing the response profile as the effect is much larger than any variation that causes.