Hi Kate,
It sounds suspiciously like your wavelength solution is the culprit. Can you you elaborate on how you’ve performed the calibration (this is an Alpy, right?). If there was a way to share your spectral and calibration images I’d be happy to take a look in ISIS.
In the mean time, I created a guide some time ago on using ISIS’ calibration assistant that may, or may not, be useful to you:
http://jazzistentialism.com/blog/wp-content/uploads/2016/10/alpy-600-mixed.pdf
Cheers,
Paul