Okay, Im working on making my centaur animations again, but i cannot export them from blender right now, this i why:

(On Right: what it looks like in blender after re-importing again all zig-zaggy (but looks fine before first export), On Left: Nifskope view)
http://img220.imageshack.us/img220/8329/badar.jpg

What I did was import the horse skeleton with idle animation, and the human skeleton with walkleft animation. then i made the animation on the horse part using the human bones are a guide for the horse ones, when i exported it, it went all weird...it is fine in blender.

ANyone know why this is happening, it doesnt seem to happen if i just make a normal animation with the horse part skeleton, or human animation, but i do get the screwy results on my centaur skeleton too...

I am totally confused on how to fix this, if anyone thinks they could have a go at fixing this, i can send blender files and nifs through a PM.

I've not been using Blender (I'm a 3DS Max person); but I've had a similar issue once before. I think it was because It was scaled and rotated in some way that NifSkope didn't understand, so NifSkope just kinda... made it up. I had limbs all over the place, and I'm not entirely sure why.
In the end, I was as stumped as you, and I couldn't be bothered to re-rig the whole thing, so I just shelved it. Sorry I can't be of more help!

EDIT: I'd suggest re-rigging the skeleton. I can't see why it wouldn't like your original shape though! Have you tried any of the sanitization functions? I can't imagine they'd do much, but still. They're always something.

thats just it, I can make animations with the skeleton just fine, but when I have the human one in there to copy from then it goes screwy.

In fact if I didnt need to match the shape of the human animation I wouldnt have a problem.

I don't understand. And I think I'll have a hard time translating blender/max. and I have no idea about your mod or your implimentation of the asset. Basically I don't know what your goal or proposed methed to achieve it.

what I am reading- you have 2 skeletons in the scene. and you import 2 different anims, which because how the mount system works- each will target a different root bone, Bip01 for the human rig, and Bip02 for the horse rig. So now you edit the animation on the horse rig to sync with what the human rig is doing in scene. Then you export the whole scene? and testing it in nifskope, the animation goes wonky.

tbh I'm stumpted. I think I'd have to atempt to recreate the senario myself in max, to be able to help. I know if I was to atempt this kind of thing, I wouldn't be expecting it to come off first time.
hope you figure it out.

Almost there.

I have the two skeletons in the scene, human one with the walking left animation and the horse one (which i use the first frame of the idle animation to get the bones into a natural position).

From here I make more frames on the horse animation that puts the horse bones in roughly the same position as the human bones as it goes through the animation. For example, when the legs are apart on the human, i move the legs apart on the horse...when they are crossed on the human, i cross them on the horse, which makes a walking left animation for the horse.

Once i have the animation done, I delete everything but the horse skeleton with its new animation, then export the animation.

At no point do the skeletons actually merge or get rigged to each other. They just are put into the same scene.

Does that make a little more sense? And yes, on export after this the bones on the horse are all wonky and weird, but it doesnt happen when only the horse skeleton is in the scene when making the animation.

I've never worked with horse skeletons, so this might be off-base, but I know with human skeletons you have to reorient the Bip01 and Bip01 NonAccum before you begin animating so that the translation data gets exported correctly. Otherwise you have elevation/rotation problems with custom animations. Does the horse skeleton have similar issues, perhaps? If so, you might want to try adapting the instructions http://cs.elderscrolls.com/constwiki/index.php/Talk:Blender/Creating_a_Character_Animation to the horse skeleton and see if that has any effect. hth

Out of curiosity, how are you implementing the centaur skeleton? Is it a custom skeleton, a 'frankenskeleton' (with bones copied and pasted between the horse/human skeletons), a centaur body implemented as a custom tail on a human skeleton? I'm afraid I haven't had the time to follow the project closely, though I think it's an extremely interesting one.

I have run into the problems with oriantation, but it doesnt really efffect the horse much (if at all in most cases). The best clue to this problem i believe is the fact that it only happens when i have had two skeletons in the same scene in blender...

The Centaur skeleton is very simple in fact, attached beside the normal Bip01 NonAccum bone now is a Bip01 NonAccumHorse Bone, which has all the horse bones in it. I did try attaching it on to the NonAccum bone, but that caused problems (rotations on the NonAccum bone casue the entire horse part to move around), so it wasnt exsactly useable.

EDIT: As i was typing this I had an idea, what if there is some shared infomation that is overwritten when i import the human skeleton, hence screwing up the horse animation. Well I imported the human skeleton first this time, then the horse and what do you know, it actually worked, it seems that whatever skeleton is imported last is the once that needs to be animated.

Glad to hear it. Thanks for the insight into the centaur skeleton. Seems like it could have quite a few applications.