The main problem with Battle Scene / Window is that you have not only to move but even to resize the command windows to make it work properly. Are you using the Standard Battle System? In that case, I could give it a look and send you a response.
Jens
EDIT: try this and let me know

It should work only with the default BS, however...
CODE
#==============================================================================
# ** Jens of Zanicuud - Resolution fix
# Paste it in materials section
#==============================================================================
class Window_Base < Window
#--------------------------------------------------------------------------
# * Constants
#--------------------------------------------------------------------------
WLH = 32
end
class Window_Help < Window_Base
#--------------------------------------------------------------------------
# * Object Initialization
#--------------------------------------------------------------------------
def initialize
super(0, 0, 640, WLH + 32)
end
end
class Window_ActorCommand < Window_Command
#--------------------------------------------------------------------------
# * Object Initialization
#--------------------------------------------------------------------------
def initialize
super(160, [], 1, 4)
self.active = false
end
end
class Window_PartyCommand < Window_Command
#--------------------------------------------------------------------------
# * Object Initialization
#--------------------------------------------------------------------------
def initialize
s1 = Vocab::fight
s2 = Vocab::escape
super(160, [s1, s2], 1, 4)
draw_item(0, true)
draw_item(1, $game_troop.can_escape)
self.active = false
end
end
class Window_BattleStatus < Window_Selectable
#--------------------------------------------------------------------------
# * Object Initialization
#--------------------------------------------------------------------------
def initialize
super(0, 0, 480, 160)
refresh
self.active = false
end
#--------------------------------------------------------------------------
# * Draw Item
# index : Item number
#--------------------------------------------------------------------------
def draw_item(index)
rect = item_rect(index)
rect.x += 4
rect.width -= 8
self.contents.clear_rect(rect)
self.contents.font.color = normal_color
actor = $game_party.members[index]
draw_actor_name(actor, 4, rect.y)
draw_actor_state(actor, 124, rect.y, 48)
draw_actor_hp(actor, 144, rect.y, 120)
draw_actor_mp(actor, 360, rect.y, 70)
end
end
class Window_TargetEnemy < Window_Command
#--------------------------------------------------------------------------
# * Object Initialization
#--------------------------------------------------------------------------
def initialize
commands = []
@enemies = []
for enemy in $game_troop.members
next unless enemy.exist?
commands.push(enemy.name)
@enemies.push(enemy)
end
super(480, commands, 2, 4)
end
end
class Scene_Battle < Scene_Base
#--------------------------------------------------------------------------
# * Create Information Display Viewport
#--------------------------------------------------------------------------
def create_info_viewport
@info_viewport = Viewport.new(0, 320, 640, 160)
@info_viewport.z = 100
@status_window = Window_BattleStatus.new
@party_command_window = Window_PartyCommand.new
@actor_command_window = Window_ActorCommand.new
@status_window.viewport = @info_viewport
@party_command_window.viewport = @info_viewport
@actor_command_window.viewport = @info_viewport
@status_window.x = 160
@actor_command_window.x = 640
@info_viewport.visible = false
end
#--------------------------------------------------------------------------
# * Update Information Display Viewport
#--------------------------------------------------------------------------
def update_info_viewport
@party_command_window.update
@actor_command_window.update
@status_window.update
if @party_command_window.active and @info_viewport.ox > 0
@info_viewport.ox -= 16
elsif @actor_command_window.active and @info_viewport.ox < 160
@info_viewport.ox += 16
end
end
#--------------------------------------------------------------------------
# * Start Skill Selection
#--------------------------------------------------------------------------
def start_skill_selection
@help_window = Window_Help.new
@skill_window = Window_Skill.new(0, 64, 640, 480, @active_battler)
@skill_window.help_window = @help_window
@actor_command_window.active = false
end
#--------------------------------------------------------------------------
# * Start Item Selection
#--------------------------------------------------------------------------
def start_item_selection
@help_window = Window_Help.new
@item_window = Window_Item.new(0, 64, 640, 256)
@item_window.help_window = @help_window
@actor_command_window.active = false
end
end
I hope this can help, in case of any errors / issues, just reply here...
Jens