Hi Lev,
I believe that the Indeo Video 5.1 codec is a new version of the Intel Indeo codec and that it is perfectly within the guidelines of Autodesk.
The reason why the Indeo Video codec isn't endorsed by Intel is because Intel sold the rights of their codec to a company named Ligos. More information can be found here:
http://www.intel.com/labs/archive/indeo.htm
and here:
http://www.ligos.com/indeo.htm
The Indeo Video 5.1 codec can be found on all modern windows pc's (I think from windows 98 and up) so there is not really a problem of Autodesk not being able to view it.
However, I can't be sure that Autodesk will accept it although I am very sure that when they said Intel Indeo codec they meant the whole Indeo line of codecs.
My animation team is encoding the animation in Quicktime because it seems to have very little quality loss. I'm using Adobe Premiere to Export Timeline as a movie and then selecting Quicktime. See if that works for you.
Well, I hope that helps! Good luck on shipping your animation!
mikeXstudios