Oh, correction, the entire screen doesn't turn that colour - only the floor tiles. The walls are all 'above' the clear_set_alpha as are the instances. 
This is the code I'm using for the surface
Viewing post in Yal's Basic Dungeon Crawler Engine comments
I think I've spotted the issue - when you set the drawing target to a surface, 0,0 is the top left corner of the surface. However, you don't always draw the surface at the 0,0 room coordinate, so drawing sprites at x,y will displace them with whatever the view top-left corner currently is. Draw the shadow sprites at x-cx, y-cy instead and it should work. (It probably worked when you did it in a separate room since you didn't move the view away from the top-left corner)