I think it has something to do with warp?
You need to write seperate scripts for the original map and to the map where the player are warped into.
You can't write down a script in one map then warp yourself to another warp and except the script will continue.
Not hacking Emerald
In Firered, you need to use Type B Script in Advanced Map to make a script continue one another.
Tutorial for it
here
I also encountered the
same problem just a couple of weeks ago