I've done some experimenting and I found that it might have something to do with the $selfillum and $selfillummask. About 70% of the materials loaded this time. The ones that didn't load either had a fucked up name or had an issue with the $selfillummask. Here's an example of the logs:
[2017.06.20-17.55.07:758]LogMaterial: Missing cached shader map for material HammUErBaseMaterial, compiling.
[2017.06.20-17.55.07:758]LogMaterial:Warning: Failed to compile Material Instance /Game/SourceStuff/Materials/BUILDINGSET057A_mat.BUILDINGSET057A_mat with Base HammUErBaseMaterial for platform PCD3D_SM5, Default Material will be used in game.
[2017.06.20-17.55.07:758]LogMaterial:Warning: (Node TextureSampleParameter2D) $selfillummask> Requires Texture2D