Ok, here is a new issue.
I will attach 2 photos. (Note: this is a demo level)
The lighter image is the way the scene is supposed to look when it is loaded. And in fact, it will load that way when I go to the scene and run it in the editor.
But if I load the level using Application.LoadLevel, it loads as the darkened image. Even if I increase the intensity of the light, the level looks completely wrong.
This is happening for all my scenes, please help!
Go to Window -> Lighting. Click on Scene tab. At the bottom uncheck 'Continuous Baking' and press Build.
This solved the problem for me when using Application.LoadLevel();