If you try ticking the fixed Y coordinate and sky not removed boxes and rerun the calibration, then click “display image” in the go tab, you will get the sum of your spectrum images with the binning zones overlaid so you can see what is happening. The objective is to have the spectra overlaying each other with the region
with the combined spectrum as narrow as possible. The spectrum binning zone should include all the spectrum region and the sky zones should include none of the spectrum region. If the spectra are not in the same Y position, with the fixed Y coordinate box unticked ISIS will attempt to track the Y movement and overlay them but as David says it may not lock onto faint spectra or with large movements between spectra.
Cheers
Robin
