Pateman

when you create a 'Pad the remaining number of weights with zero' are you also setting the bone ID to something valid?

Yes, I set it to zero, then in the shader I verify whether the bone ID is set to 0, like so:

mat4 getBoneMatrix(int boneIndex) {
   mat4 retMat = mat4(1.0);
   if (boneIDs[boneIndex] != 0) {
      retMat = boneMatrices[boneIDs[boneIndex]];
   }
   return retMat;   
}

float getWeight(int boneIndex) {
   float res = 1.0;
   if (boneIDs[boneIndex] != 0) {
      res = boneWeights[boneIndex];
   }
   return res;
}