Thanks for the response!

I'm not sure why you have a seperate "skinMatrix" and "transformMatrix" being applied to the animation:

The .x file has a skinWeights section, in that it has a matrix, that's the skinMatrix I'm referring to. The transformMatrix is where I'm storing the result of all the matrix operations.

Export your vertex data post-transformed, so that the model looks correct when skinned with identity matricies.

I'm doing that. If I set my bone matrices to identity, I get the model as it looks in Blender.

Export the inverse of the worldspace bind pose for each joint.

Is the worldspace bind pose the same as the bind pose used to transform the vertices to get the "post-transformed vertex data"? i.e. The matrix obtained by rootMatrix*modelMatrix? If so the bind pose is the same for each joint... so I don't understand.

So you're saying the animation matrix should be created like the following?

   Matrix4f animationTransform = new Quaternion(rotation).toMatrix();
   animationTransform.m00 *= scale.x;
   animationTransform.m01 *= scale.x;
   animationTransform.m02 *= scale.x;
  
   animationTransform.m10 *= scale.y;
   animationTransform.m11 *= scale.y;
   animationTransform.m12 *= scale.y;
  
   animationTransform.m20 *= scale.z;
   animationTransform.m21 *= scale.z;
   animationTransform.m22 *= scale.z;
  
   animationTransform.m30 = position.x;
   animationTransform.m31 = position.y;
   animationTransform.m32 = position.z;

Where does the armatureMatrix and parent animation transforms come into play?

I know that

   Matrix4f.mul(transformMatrix, boneMatrix, transformMatrix);
   Matrix4f.mul(transformMatrix, skinMatrix, transformMatrix);

Results in the identity matrix. But if I multiply in the animationTransform from above, things get wonky. I made an animation that's just the bind pose. But the animationTransform is not the identity matrix when the model is in the bind pose, so what's the deal?

Thanks for the response!

I'm not sure why you have a seperate "skinMatrix" and "transformMatrix" being applied to the animation:

The .x file has a skinWeights section, in that it has a matrix, that's the skinMatrix I'm referring to. The transformMatrix is where I'm storing the result of all the matrix operations.

Export your vertex data post-transformed, so that the model looks correct when skinned with identity matricies.

I'm doing that. If I set my bone matrices to identity, I get the model as it looks in Blender.

Export the inverse of the worldspace bind pose for each joint.

Is the worldspace bind pose the same as the bind pose used to transform the vertices to get the "post-transformed vertex data"? i.e. The matrix obtained by rootMatrix*modelMatrix? If so the bind pose is the same for each joint... so I don't understand.

So you're saying the animation matrix should be created like the following?

   Matrix4f animationTransform = new Quaternion(rotation).toMatrix();
   animationTransform.m00 *= scale.x;
   animationTransform.m01 *= scale.x;
   animationTransform.m02 *= scale.x;
  
   animationTransform.m10 *= scale.y;
   animationTransform.m11 *= scale.y;
   animationTransform.m12 *= scale.y;
  
   animationTransform.m20 *= scale.z;
   animationTransform.m21 *= scale.z;
   animationTransform.m22 *= scale.z;
  
   animationTransform.m30 = position.x;
   animationTransform.m31 = position.y;
   animationTransform.m32 = position.z;

Where does the armatureMatrix and parent animation transforms come into play?