What is the output from Scalepack? Does it contain I & Isig or F & Fsig? Why are there some negative values for I (or F) in the output file?
Output from Scalepack is I, sig(I), where I refers to Lorentz, polarization etc. corrected diffraction intensity. Sometimes this I is referred to as F**2. Even the best (averaged) estimate of intensity may be negative - see discussion of sigma cutoff keyword in Scalepack Keyword Description.