CROP messes up latitude/longitude values for Rosetta data

I am working with Rosetta images and trying to use CROP, but it messes up the latitude-longitude values even with PROPSPICE parameter checked. The Rosetta images were converted from .IMG to .cub using rososiris2isis, and then SPICE information was added to them using spiceinit. The latitude longitude values at this level are perfect, but when I try cropping these cubs, it gets a completely different latitude longitude values.

Any idea what may be going wrong?