I got a testfile for this problem and I think I have fixed the problem. The problem occured if item 401 was in the EXTH header and had length 1. I had mistakenly assumed it should have length 4. Things that happens when the format is not documented.
it is probably good to make these assumption. They willl cause bugs but I will get feedback and more data to use to try to figure out what is wrong. So whenever you see something like:
ERROR: generated EXTH does not match original
in the output from mobi2mobi please tell me and if possible send me the file that caused this.
There is a version 0.0.23 available as tar file but the only change is the one described here so no need to update if you do not have this problem.