We have 30 characters of all different sizes, men women and children. They're all bound in a T pose in maya and exported as a static fbx. We have one anim clip that works fine on male characters, but all the other characters stretch up to fit the anim clip.

When we reimport these fbxs into Maya they work fine, the joints are reading rotations on a scaled rig. In Houdini, the joints match the positions of the anim clip, resulting in a small child stretching out to 180cm tall.

Is there a way to prevent the joint stretching in the agents?

It's hard to tell, but I'd try logging a bug if there's a difference when directly loading into agents.