contact Tazpn or Shon at the niftools forums.
http:\\niftools.sourceforge.net\forums
I told them about that too, and they're aware of some bugs when you export directly with max 9. if you have nifskope, I'd try to build the skeleton on nifskope by scratch.
export your model to .3ds or .obj from max, and import it into nifskope.
to understand how the hierarchy works, open a ship .nif in nifskope and write down which nodes inherit other nodes. then, add or move nodes until you get the skeleton in your imported .3ds/obj similar to the .nif you opened.
BTW: it's impossible there is nothing about those errors in the error report forums, third forum block, below the main header. the forum called "3ds max plugin help and bug reports". also, there is a search function there for something, so make use of it.