Came across this while looking up the BIO situation at 1Y2. For reference, the fix Koji mentions can be seen in the attached screenshot (one example, the other BIO cards also have a similar fix). The 16th bit of the BIO is grounded, and some bit-shifting magic is used to implement the desired output.
Yutaro talked about the BIO bug in KAGRA elog. http://klog.icrr.u-tokyo.ac.jp/osl/?r=9536
I think I made the similar change for the 40m model somewhere (don't remember), but be aware of the presense of this bug.