Not sure what the issue us with the updated DWIConvert (i.e. why it would not take unsigned short data). Assuming that your DWI data does not have intensity values above 32,000 , you could simply convert the QCed unsigned short DWI file to a signed short one using unu (a swiss-army-knife style utility for NRRD that is packaged with Slicer):
unu convert -t short -clamp -i inputUnsignedShort.nrrd -o outputShort.nrrd

Best
Martin