Reposting here for better visibility/applicability.

I have discovered a fix for problems with green colored ships etc in mods. It is not an easy fix, so this needs to be done by workshop maintainers and mod makers, although users can attempt it as well if they want.

The cause of the problem is Shaders. Since the update, custom shaders have not been automatically compiled by the game, so ships show up green (the default shader). Uncompiled shaders have the file extension .fx and .fxh instead of .fxo.

Mod shaders are located in the Data/Art/Shaders directory of the mod. Workshop mods are located in steamapps/workshop/content/32470 and then are in numbered folders. Other mods are located in the game's local files.

To fix the problem, mod makers and workshop maintainers need to COMPILE their shaders.

1) Go to https://www.microsoft.com/en-us/download/confirmation.aspx?id=6812 and acquire the Microsoft DirectX Software Development Kit

2) Either install the SDK or open the installer with an archive reader like 7-Zip

3) Go to the Utilities/bin folder and find the program fxc.exe

4) Put fxc.exe where you have uncompiled shaders

5) Open Command Prompt and make sure it is set to the directory where your fxc.exe and shaders are (so if you run fxc.exe /? you get help text)

6) Run the command fxc.exe /Tfx_2_0 /LD /Fo"ShaderOutputName.fxo" "ShaderInputName.fx"

7) Your compiled .fxo shader should be in the same folder as fxc.exe. Now you can put it in your mod, Data/Art/Shaders folder and the game should read it in.

8) Run the mod and check that models look normal

To Petroglyph: it seems that you removed calls to D3DCompileFromFile when you updated the game executable. I'm not sure how realistic it is to put back in.