well in the case of canon cameras anyway, SGP is scaling the data coming from the camera from the native 14-bit data to 16-bits when it writes out the fits file. this means that if you have a bunch of CR2s or fits files produced with pixinsight, they will not be compatible as pixinsight does not scale the data. i don't know what other packages might or might not do.
i'm not sure about NEF files because i've never worked with a nikon camera but if they are also 14-bit then you'll have the same issue.
rob
