I imported a quadruped character using FBX Character Import. The animation previews correctly with Joint Deform, however, when I add an Agent Clip, the agent rotates 90° on x and scales 100x larger.
In the attachment below, the first geo is the agent manually scaled down*0.01 and the second one is the deformed geo with joint deform.

Just a guess, but the capture pose output from FBX Character Import doesn't necessarily include all of the skeleton's joints, just the ones used for skinning
If that's the case, using it as the input to the Agent from Rig SOP means that the agent's skeleton will be missing some joints, which could explain animation issues

That was infact the issue! I got the rest pose of the animated skeleton via fbx animation import, isolated the root and merged, parented it with the capture skeleton joints and the issue was resolved!
Thanks!

I think you could also likely just use the rest pose directly, rather than merging it into the capture skeleton

The input to the Agent from Rig SOP is just used as the agent's rest pose (e.g. the pose used as a fallback when there isn't any animation assigned to the agent) and doesn't need to be the capture pose
The capture pose can be wired into the third input of the Agent from Rig SOP when adding a shape

Right that works as well! Thanks!