In my opinion you have several issues with your code, try something like this :

private static void BoneDraw(Model model)
{
	const float width = 1f;
	var bones = model.Bones;
	
// define new array
	var bonesHasBeenDrawn =... // !!!


// first pass: draw parent->child bones !
	foreach(var bone in bones)
	{
		var parent = bone.Parent;

		if(parent != null && boneHasBeenDrawn[parent.Number]!=true ) // !!!
		{
			var boneMatrix = model.FinalBoneMatrices[bone.Number];
			var parentMatrix = model.FinalBoneMatrices[parent.Number];



//handle the parent bone, not the bone ! therfor swap parent and bone here
			var length = Vector3.Distance(parentMatrix.TranslationVector, boneMatrix.TranslationVector);
	    var dir = Vector3.Normalize(boneMatrix.TranslationVector-parentMatrix.TranslationVector); // !!!
			var center = parentMatrix.TranslationVector + dir * length / 2; // !!!
			
			
			var box = new Box(center, length, width, width);
// use the parent here !
			var temp = Matrix3X3.CreateFromMatrix(parentMatrix); //!!!

			box.OrientationMatrix = temp;

			DeferredRenderer.ModelDrawer.Add(box);
			boneBoxDictionary[bone.Number] = box;
			
// done
			boneHasBeenDrawn[parent.Number] = true;
		}
	}
	
// second pass: draw bones without child and therefor without known length
	foreach(var bone in bones)
	{

		if(boneHasBeenDrawn[bone.Number]!=true )
		{
			var boneMatrix = model.FinalBoneMatrices[bone.Number];

//virtual length
			var length = 1.0; // default length for unknown bones

// point along z-axis, or whatever your lookat axis is
			var center = boneMatrix.TranslationVector + boneMatrix.LookAtVector * length *0.5 ;
			
			
			var box = new Box(center, length, width, width);
// use the parent her !
			var temp = Matrix3X3.CreateFromMatrix(boneMatrix);

			box.OrientationMatrix = temp;

			DeferredRenderer.ModelDrawer.Add(box);
			boneBoxDictionary[bone.Number] = box;
			
// done
			boneHasBeenDrawn[bone.Number] = true;
		}
	}
	
}

First of, if you take the parent bone as direction, then you are actually drawing the parent bone and you need to orient it relative to it and not to the current bone. The second issue is, that you dont handle leaf-bone with it, therefor you need to draw the leaf-bones with an virtual length (the length is unknown).

The problem is, that bones are just a transformation matrix, without any length (this is more or less cosmetic in the modelling tool). Therefor you will have an issue with your approach, if the bones are not directly connected to its parents (this is the case if you model the bones with an offset). The lookat vector of the your bone matrix is most likely either the Y or the Z vector and it would be better in this case to use it instead of the difference vector between bone and parent. In other words, the second pass for all bones would be the more accurate way to do it.

I'm still not sure which vector you're referring to exactly, so I tried the Forward/Up/Right vectors from the parent matrix, and also tried a few like this:

It is the vector, the bones are pointing along. A bone is eventually only a transformation matrix, the representation in the modelling tool will draw the bone starting at the transformation matrix and point along one axis of it (eg. z-axis, but this depends on the modelling tool). It is important, that the direction of the bone depends only on the final transform matrix of bone and not on the parent transform. The only useful thing is, that you could use the relationship between parent and child to guess the length of a bone, but this only works for 'connected' bones.

You should start with the bones and a virtual length of eg 1 (or some other useful, displayable length) and leave the parent out of it completly. Try to get the orientation of the bones right in the first place, once this has been done, try to optimize the length by looking at the parent-child relationshipment.

Something like this:

	foreach(var bone in bones)
	{
			var boneMatrix = model.FinalBoneMatrices[bone.Number];
			var length = 1.0; // default length for unknown bones

// point along z-axis, or whatever your lookat axis is
			var center = boneMatrix.TranslationVector + boneMatrix.Forward* length *0.5 ;
			
			var box = new Box(center, length, width, width);
// use the parent her !
			var temp = Matrix3X3.CreateFromMatrix(boneMatrix);

			box.OrientationMatrix = temp;

			DeferredRenderer.ModelDrawer.Add(box);
			boneBoxDictionary[bone.Number] = box;
	}

To be honest, there seems to be something else wrong. I would expect kind of symmetrically build up according to the maya model, but there are some clear asymmetrically bones (leg,arms,hips). So, the question is, is the skeletal animation system working at all ? Is your box rendering code ok ? Eg the green bone at the right arm is quite off, the same could be say about the left green leg bone, why ?