Did you copy all the code in the teleporting to 1999?
If you don't have the first two (setting 7E028F and 7E027E), then the characters can be seen at the ground in a solid shore, and control will go there when you land. I've also at times just simply had the game freeze up on me. Try again.
On another note, I modified the 1999 AD palette set, and gave the first dactyl a new palette.
1999 AD's palette is compressed at 3D35F.
I added 2 16-color palettes to it. Only the second one changed the dactyl.