maybe I'm clutching at straws here but could the bone priorities be an issue? I haven't actually set any yet.
Maybe. The horse "mount" animation, for one, includes the human Bip01 bones in it. I saw that the horse's "mount" animation had all the bones in it set to a priority of "61", which is higher than the human idle.kf and walkforward.kf (and many other human anims).
Animations with a higher priority, are able to supercede lower priority animations, or something like that.
So it might be that if are walking up to a horse with walkforward.kf with priority of 30 and activate the horse to get on it, and if the "mount" animation has bones with priority of 0, it *might* be messing things up, because maybe the human Bip01 bones referenced in the horse mount animation aren't being overridden by the horse mount anim.
But your picture of the human sitting and badly rotated on the creature - the human on the creature looks like he was already animated in mount position, save for that bad rotation....so this might not be the case.
Either way, it can't hurt to try changing the bone priorities using the kfupdater utility (it works for Oblivion, too):http://www.fallout3nexus.com/downloads/file.php?id=496
Koniption