Well what about using an older CHDman...that app that I got your help on a year ago, well Q&A really...I was reverting Dreamcast GDI CHD's fine after you corrected me about the endian issue, all hash's turned out fine.
Granted I needed a ClrMamePro Dat of the original dumps, since the CHDman of the day created just a CUE and a monolithic BIN file, so I had to slice and dice, then change the endian on the proper tracks...but the result was matching hash's to that of the original dump.
Was there something done different with Naomi & Atomiswave GDI's?