Referenced script on this behaviour is missing - Strange

I've had this error many times before, and have been able to find the offending script that's disappeared, but this time I have no idea.

Currently, when I open a scene using Application.LoadLevel(), I get 432 referenced script missing warnings.

What's strange is that, when I open the scene up in the editor and press play, not a single warning appears.

The same thing happens when I create a blank scene with only a button, which loads the warning-filled scene.

Any help on this would be much appreciated!