Material Slot Order

In HD2, the slot of the material determines what vertex groups are assigned to what bones on the armature.

This means that if all the weights are assigned to material slot 2, assigning the material you are using for your mesh to slot 1 will cause the weights to be completely wrong.

To demonstrate this, let's take the I-102 Brawny Arm Right. You can see in the picture below that the gore material is 12070197922454493211. (This is the same across all armor sets.) It is currently occupying material slot 1.

The gore material is only weighted to a single bone usually, while the other material will be the actual material of the arm that is weighted to the other bones of the HD2 armature. The actual mesh material is occupying material slot 2.

If I swap these material slots around this will happen in-game.

WARNING

Material slot order is different for every armor set per body part per body type. There is no consistency between the armor sets so you will need to check the base game part you are replacing to ensure you have the correct material slot order

This is not exclusive to armor sets and can also be found on enemies and weapons as well.