Hoping for some advice, things to check.
I have In rv901t board running, correct firmware, i disabled most os the mdb2hal stuff in hal to get it to run. I have modded the board as posted on this post, the j601 port works for outputs and tests well. However the j600 port isn't working as input. If i mod my hal file so one of the inputs (on the j600 port) is an output it works as one. ( setp ***** is_output true. - or something like that) shouldn't the firmware be setting it as input?
edit # found the problem, page 8 note that the bit file on github is not suited to a modded board. So use your own created bitfile or the page 8 one.