Did you put any scripts into your game?
If you don't have any specific information, it's unlikely that anyone will know how to help you. What happened before this change occured? I highly doubt that there is nothing you added, because something is obviously effecting the battle sequence and this is not a problem in stock essentials.
What about PBS data? did you modify Pokemon.txt at all?
Yeah, but all the PBS file did was add the abilities if I'm not mistaken...