I downloaded your cap, but there's too much going on. Noone but you knows the concept, so I can't say what exactly you are trying to achieve. Could you please do a simple example cap with an explanation where exactly it does not work as intended?
About ScrollX and ScrollY: They return the center point of the current view. If you don't scroll your layout, then those values never change.
Window size 640x480, layout size 640x480
ScrollX, ScrollY will always return 320, 240
Window size 640x480, layout size 800x600
ScrollX, ScrollY will return 320, 240
If you now scroll your layout, using System: Scroll to X 420 then
ScrollX, ScrollY will return 420, 240
I made an another simple example cap... well i'm not sure about your methods, i tried to experiment with another methods and it works!
What do you think about this method? I'm unaware about layout editor may support to fit the 3000 height sprite or 800 height separated sprites at vertical align...
Actually, i had no idea how to make it when the boss appears should to stop vertical scrolling except a tilemap with animated offset (If you saw my first post). Until The boss dies and the continue vertical scrolling.
Do you think can you help?
Sorry, my english is not native language, i hope you understand.