When a RM2K battle has a script attached that shows MessageBoxes, then the last Input Key press will carry over to the "Action" scene (selection between Fight, AutoBattle, Escape) and thus automatically select the first input.
One has to explicitly press Cancel every time to select either AutoBattle or Escape because the first option will always be taken.

I compared the behavior with RPG_RT (up-to-date RM2KE) and this doesn't happen there.