It might be that the "border" attribute edits both left-right and up-down borders. Because of this you are experiencing a larger border on all the sides of the battle panel box.
To solve this you should find a way to edit only the left side, or even to automatically center the box without even changing border's value.
Honestly I've never tried to edit an xml for PokéMMO so I can't really help by telling you how it should be written, but the least I can do is to explain why this is happening.