GOM ... I hadn't re-zeroed the bones after I moved the mesh..I will give that a try tonight. If it works, it will be great! Every other element in the unusual skeleton department is working OK now, and KE is making big steps getting animation CAS files into Max along with MS3D models. That will make key-framing a lot easier for me, since Max lets you input a rotation angle, rather than forcing you to manually move.

If it fails, I will post back and give details. If oyu want any more data, just shout. I can PM you a whole raft of test stuff that KE and I have been batting back and forwards in an effort to understand why things work or don;t work here. The only bit left is to work out why, whem I move JUST THE MESH from a horse skeleton, the animations still work, but the mesh falls off the bones in really odd ways. In the MS3D file ( pre conversion ) the bones are not touched. I just moved the mesh to one side, leaving rigging, bones etc where they were. The Horse breaks when you do this.

I found this out when I tried to rig a new mesh with double horse models to a single horse skeleton. It broke as above. I couldn't figure out what was wrong....and ultimately I pinned it down to a model that was not sitting exactly ON TOP of the skeleton.

As soon as I started rigging vertices to a bone that the mesh wasn't sitting over, this happened. I suspected my model ... so I used a stock horse, and moved the mesh to one side to simulate what I had done with the complete mesh. I got exactly the same problem.
When I did the same to a camel or elephant..they were fine! Something in the horse data meant I could not do this. We have been trying to isolate what the problem might be ... so far without much success.