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Hiya! Sorry for taking so long to reply.

It sounds like there's an issue with the depth sorting between obj_skyboxcontrol and the other objects... drawing has a bunch of odd quirks in GMS2 compared to previous versions, e.g. depth sorting doesn't work in Draw GUI event. Looks like ortho and perspective drawing are drawn in separate passes so ortho always is drawn last. To just get the track to draw properly, you could try commenting out the code in the Draw event of the obj_skyboxcontrol object. (You might wanna set up a background color in the room instead as a placeholder so that the window gets cleared each draw frame).

Not sure what the best way to solve the problem is, depends a bit on what graphical style you wanna go for in your game. If you want a stylish celshaded look you could keep a solid background color, for a more realistic style you could add some code in e.g. stage_model_create() so that it creates a skybox as well (the simplest approach would be to just add walls at the X and Y boundaries but it might look a bit flat). You can make texture atlases bigger than 2x2 (to add in some new sky textures etc), just don't forget to update the atlas-size arguments to stage_model_create() so that it gets the correct size - there's no info in the graphic asset that can be used for this so it needs to be provided off-band.