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Tested with dcraw_emu -T -w,

Tested with dcraw_emu -T -w, for both 0.20-stable branch (from github) and for master branch (also from github).
I do not see great color difference here:

Files produced are also (temp.) stored on dropbox for your inspection:

Please try to reproduce the problem using LibRaw's sample application (dcraw_emu or simple_dcraw). If these applications produces correct results, the problem source is probably in your code or in Java wrapper you use.

-- Alex Tutubalin @LibRaw LLC