A move animation includes all the move's animation cels, and also cels for the user and target Pokémon. The animation itself revolves around two fixed points (corresponding to those of the user and the target), which have default values (corresponding to the two battlers' positions in a single battle for convenience). These fixed points are then set when using the animation depending on the actual positions of the user and target, and the animation's cels shifted around them accordingly.
I'll describe what you should edit in the latest version.
In PokemonAnimEditor, find the def play and swap out the quoted-out numbers. That makes the fixed points depend properly on the test battler positions while playing the animation in the Animation Editor. Then, in PBAnimation, switch out the numbers again in the defs pbConvertRPGAnimation and addFrame. That sets the default fixed points when creating frames/compiling animations. Finally, do the same in PokeBattle_ActualScene, def pbAnimationCore. That makes the fixed points depend properly on the battler positions in actual battles.
That's all the scripting you'll need to do, I think (it's a complex thing and I may have forgotten something). However, you'll still have a PkmnAnimations.rxdata file containing animations with the wrong fixed points. Delete it, and let the game compile the animations from the Database (there's currently no difference between the two).
See if that works. The way animations work sounds fiddly, but it makes sense.