I found the solution. The previous scene needs to transition out first, then the background, then all characters and overlays are positioned with the & (Don’t use @), lastly transition in.
Example:
@transition fade out black in 3
INT. BACKGROUND
&overlay CLUB TABLE shifts to -21 -47 in zone 1
&overlay CLUB TABLE scales to 0.337 0.337
&overlay CLUB TABLE moves to layer 2
&CHARACTER spot 0.917 229 162 in zone 1
&CHARACTER moves to layer 1