Do you have a background layer as well? I've had a few people send me similar things after the newest GM update. Looks like the background isn't clearing. You could try (in a pre-draw event) to do:

surface_set_target(application_surface);
draw_clear(c_black);
surface_reset_target();

Maybe that will solve the issue? I will look into this further!

Edit

• Check that 'Clear display buffer' is ON
• Also, you could just draw a black rectangle behind everything in the RenderPipeline draw event right before the script pipeline_render() and set the z-writing to false like so:

gpu_set_ztestenable(false);
gpu_set_zwriteenable(false);
draw_set_color(c_black);
draw_rectangle(0,0,window_get_width(), window_get_height(), false);
gpu_set_ztestenable(true);
gpu_set_zwriteenable(true);

I can't seem to re-create the issue. I followed the guide again (just to make sure) and it works as expected.

You can Download a test project I made up until figure 7 & 8. Not exactly sure what's going on? O_o