So I unchecked "Initially Visible" on every layer, then re-checked each layer 1 by 1. Each layer came back visible until I got to my HUD layer, which is on top. When I rechecked the HUD layer everything went Orange again
So now the question is why is my HUD layer covering everything under it with the Project Background?
Ah yes, quite the simple fix. Allow me to explain:
One of the objects on your HUD is set to "Source In"
Just change it to normal and your problem will be fixed :)