Hi Kate,
It is one of the idiosyncrasies of ISIS calibration for the Alpy that you have to tweak the value of the pixel size. This goes against common sense as of course the pixel size is fixed.
I think this is because no 2 Alpys are quite identical, and is due to minor differences in focal lengths and chip to grism distances. François Cochard explained this at the BAA workshop far better than I can remember it now, but I remember that tweaking the pixel size fixes the problem.
Best wishes,
Andy