Blend Indices Are Empty After Migrating To Monogame

I am migrating an XNA 4 project to MonoGame. I have a problem with a skinned shader, the blendindices have zero values when passed to the vertex shader. I have used colored pixel debugging to determine this, and compared the results with the original XNA project.

The shader was upgraded from SM 2 to SM 4 during the migration.

The vertex buffer contains the expected values before the Draw call.
Here is the input struct which is contained in the vertex buffer:

 // This is passed into our vertex shader from Xna
    struct VS_INPUT
    {
// This is the position of the vertex in the model file
float4 position : SV_Position;

// The vertex normal
float3 normal : NORMAL0;

// This is the texture coordinate for the vertex in the model file
float2 texcoord : TEXCOORD0;

// These are the indices (4 of them) that index the bones that affect
// this vertex.  The indices refer to the MatrixPalette.
half4 indices : BLENDINDICES0;

// These are the weights (4 of them) that determine how much each bone
// affects this vertex.
float4 weights : BLENDWEIGHT0;
    };

In the model processor, the blend indices for each vertex are packed into a Byte4 struct like so:

 Vector4 bi = new Vector4();
 bi.X = count > 0 ? indexer.GetBoneIndex(bwc[0].BoneName) : (byte)0;
 bi.Y = count > 1 ? indexer.GetBoneIndex(bwc[1].BoneName) : (byte)0;
 bi.Z = count > 2 ? indexer.GetBoneIndex(bwc[2].BoneName) : (byte)0;
 bi.W = count > 3 ? indexer.GetBoneIndex(bwc[3].BoneName) : (byte)0;
 indicesToAdd[i] = new Byte4(bi);