George,

I have not been able to reproduce your scenario here
(it has been working correctly for me). What orientation
are you starting with before transforming to ANALYZE?
You can check it with "3dinfo t2+orig | grep orient".

You are welcomed to upload those datasets via the link
'Upload Data', above our messages. I'll try it out with
the same commands that you have used.

More importantly, I recall that some changes were made
to that part of the code by Rich Hammett. So if you are
seeing a problem, he may have already fixed it. It might
be worth you while to download new binaries and try
again.

In any case, feel free to upload those datasets, along with
the commands you used. I would be happy to take a look.

- rick