Well thanks for responding because it made me investigate a bit further and I discovered that I was actually using 0.9.2 from my /usr/local/bin... With the proper 0.9.5 version in use and the following command everything is working as expected.
Code:
HandBrakeCLI -f mkv -e x264 --crop --strict-anamorphic -q 20 -a 1,1 -E faac,ac3 -6 dpl2,auto -R 48,auto -B 160,auto -D 2,2 -d slower -s 1,2,3,4,5 -x ref=2:bframes=2:subme=6:mixed-refs=0:weightb=0:8x8dct=0:trellis=0 -v -i input.iso -o output.mkv