Why does Fallout 4 load with broken textures?

Found a solution. It is indeed "Godrays".

Unfortunately, even if you turn them off the game doesn't fully turn them off so you have to turn them off in the ini.

Go to Fallout4Pref.ini

Under [Display] change the following to exactly this: iVolumetricLightingQuality=0 bVolumetricLightingEnable=0

After you change them both to 0, save the file.

Then go to the properties and make it read only. If you do not change it to "Read Only" Fallout will automatically switch this setting back.

Launch Fallout and enjoy it Rainbow free.

The problem is located with the Shadow Shaders in the game, these 2 settings were introduced for AMD GPUs because NVIDIA had this setting built in. After 1.3 for some reason it broke and the God Rays break the shadow shader for some reason. Its much more complicated than this, but I say this just to make a long story short.

The problem isn't in the textures themselves, but the way shadows interact with the surface textures.

I am unsure if this will fix your other graphical issues, but this should at least fix the rainbow problem.

So after a while I've narrowed it down to either an error with my NVIDIA Card and/or error with the Intel graphics card.

To fix the problem with broken textures I completely uninstalled by NVIDIA and Intel graphics followed by redownloading and updating the graphics card.

Since uninstalling and reinstalling the graphics cards I have not had a problem with the textures in Fallout 4.