Missing a bit ?

So this software guy gave me software that uses libraw to convert my Canon CR2 files into 16-bit Tiffs. The problem is that the resulting Tiff is half as bright, and when I compare the values between the two files in Canon's digital photo 'professional' software, I can see that the Tiff file shows values for red green and blue which are half-or-less than the values shown in the CR2 file. It's as if the most significant bit somehow got stripped off. Anyone seen this???