Well, there are two Input.ini files. BaseInput.ini and DefaultInput.ini. When I looked at them they were both already set as "read only" so I tried taking that off and setting the controls. Still reverted as soon as I got as far as the main menu from the controls section. The files didn't show any change after swapping the controls either. So I tried setting the controls and then setting the files to "read only." controls still reverted. here's the BaseInput.ini text if anyone cares to look through it who knows how to fix it.
[Engine.PlayerInput]
MoveForwardSpeed=1200
MoveStrafeSpeed=1200
LookRightScale=300
LookUpScale=-250
MouseSensitivity=60.0
DoubleClickTime=0.250000
bEnableMouseSmoothing=true
; --- General bindings
Bindings=(Name="Fire",Command="Button bFire | StartFire | OnRelease StopFire")
Bindings=(Name="AltFire",Command="StartAltFire | OnRelease StopAltFire")
Bindings=(Name="MoveForward",Command="Axis aBaseY Speed=1.0")
Bindings=(Name="MoveBackward",Command="Axis aBaseY Speed=-1.0")
Bindings=(Name="TurnLeft",Command="Axis aBaseX Speed=-200.0 AbsoluteAxis=100")
Bindings=(Name="TurnRight",Command="Axis aBaseX Speed=+200.0 AbsoluteAxis=100")
Bindings=(Name="StrafeLeft",Command="Axis aStrafe Speed=-1.0")
Bindings=(Name="StrafeRight",Command="Axis aStrafe Speed=+1.0")
Bindings=(Name="Jump",Command="Jump | Axis aUp Speed=+1.0 AbsoluteAxis=100")
Bindings=(Name="Duck",Command="Button bDuck | Axis aUp Speed=-1.0 AbsoluteAxis=100")
Bindings=(Name="Look",Command="Button bLook")
Bindings=(Name="Pause",Command="Pause")
Bindings=(Name="LookToggle",Command="Toggle bLook")
Bindings=(Name="LookUp",Command="Axis aLookUp Speed=+25.0 AbsoluteAxis=100")
Bindings=(Name="LookDown",Command="Axis aLookUp Speed=-25.0 AbsoluteAxis=100")
Bindings=(Name="CenterView",Command="Button bSnapLevel")
Bindings=(Name="Walking",Command="Button bRun")
Bindings=(Name="Strafe",Command="Button bStrafe")
Bindings=(Name="NextWeapon",Command="NextWeapon")
Bindings=(Name="ViewTeam",Command="ViewClass Pawn")
Bindings=(Name="TurnToNearest",Command="Button bTurnToNearest")
Bindings=(Name="Turn180",Command="Button bTurn180")
Bindings=(Name="W",Command="MoveForward")
Bindings=(Name="S",Command="MoveBackward")
Bindings=(Name="A",Command="StrafeLeft")
Bindings=(Name="D",Command="StrafeRight")
Bindings=(Name="F",Command="FreezeRendering")
Bindings=(Name="MouseX",Command="Count bXAxis | Axis aMouseX")
Bindings=(Name="MouseY",Command="Count bYAxis | Axis aMouseY")
Bindings=(Name="LeftMouseButton",Command="Fire")
Bindings=(Name="RightMouseButton",Command="AltFire")
Bindings=(Name="LeftControl",Command="Jump")
Bindings=(Name="SpaceBar",Command="Jump")
Bindings=(Name="BackSpace",Command="Jump")
Bindings=(Name="Escape",Command="CloseEditorViewport | onrelease ShowMenu")
Bindings=(Name="E",Command="Use")
Bindings=(Name="MouseScrollUp",Command="PrevWeapon")
Bindings=(Name="MouseScrollDown",Command="NextWeapon")
Bindings=(Name="C",Command="DoDuck")
Bindings=(Name="P",Command="TogglePhysicsMode")
Bindings=(Name="Up",Command="MoveForward")
Bindings=(Name="Down",Command="MoveBackward")
Bindings=(Name="Left",Command="TurnLeft")
Bindings=(Name="Right",Command="TurnRight")
Bindings=(Name="LeftShift",Command="Walking")
Bindings=(Name="F1",Command="viewmode wireframe")
Bindings=(Name="F2",Command="viewmode unlit")
Bindings=(Name="F3",Command="viewmode lit")
Bindings=(Name="F5",Command="quicksave")
Bindings=(Name="F6",Command="quickload")
Bindings=(Name="F7",Command="set D3DRenderDevice bUsePostProcessEffects False",Control=False,Shift=False,Alt=False)
Bindings=(Name="F8",Command="set D3DRenderDevice bUsePostProcessEffects True",Control=False,Shift=False,Alt=False)
Bindings=(Name="F9",Command="shot")
Bindings=(Name="F10",Command="dumpdynamicshadowstats")
; --- Camera binds
Bindings=(Name="Delete",Command="Camera Default")
Bindings=(Name="End",Command="Camera FirstPerson")
Bindings=(Name="PageDown",Command="Camera ThirdPerson")
Bindings=(Name="PageUp",Command="Camera Fixed")
Bindings=(Name="Home",Command="Camera FixedTracking")
Bindings=(Name="Insert",Command="Camera FreeCam")
; --- XBox Bindings
Bindings=(Name="XboxTypeS_A",Command="Use")
Bindings=(Name="XboxTypeS_B",Command="Jump")
Bindings=(Name="XboxTypeS_X",Command="ChangePosture")
Bindings=(Name="XboxTypeS_Y",Command="NextWeapon")
Bindings=(Name="XboxTypeS_Back",Command="")
Bindings=(Name="XboxTypeS_Start",Command="|onrelease showmenu")
Bindings=(Name="XboxTypeS_LeftShoulder",Command="obj list")
Bindings=(Name="XboxTypeS_RightShoulder",Command="mem")
Bindings=(Name="XboxTypeS_DPad_Up",Command="MoveForward")
Bindings=(Name="XboxTypeS_DPad_Down",Command="MoveBackward")
Bindings=(Name="XboxTypeS_DPad_Left",Command="TurnLeft")
Bindings=(Name="XboxTypeS_DPad_Right",Command="TurnRight")
Bindings=(Name="XboxTypeS_RightTrigger",Command="Fire")
Bindings=(Name="XboxTypeS_LeftTrigger",Command="ToggleTargetingMode")
Bindings=(Name="XboxTypeS_LeftX",Command="Axis aStrafe Speed=1.0 DeadZone=0.3")
Bindings=(Name="XboxTypeS_LeftY",Command="Axis aBaseY Speed=1.0 DeadZone=0.3")
Bindings=(Name="XboxTypeS_RightX",Command="Axis aTurn Speed=1.0 DeadZone=0.2")
Bindings=(Name="XboxTypeS_RightY",Command="Axis aLookup Speed=0.8 DeadZone=0.2")
[Engine.DebugCameraInput]
Bindings=(Name="MoveUp",Command="Axis aUp Speed=1.0")
Bindings=(Name="MoveDown",Command="Axis aUp Speed=-1.0")
Bindings=(Name="MoveForward",Command="Axis aBaseY Speed=1.0")
Bindings=(Name="MoveBackward",Command="Axis aBaseY Speed=-1.0")
Bindings=(Name="TurnLeft",Command="Axis aBaseX Speed=-200.0 AbsoluteAxis=100")
Bindings=(Name="TurnRight",Command="Axis aBaseX Speed=+200.0 AbsoluteAxis=100")
Bindings=(Name="StrafeLeft",Command="Axis aStrafe Speed=-1.0")
Bindings=(Name="StrafeRight",Command="Axis aStrafe Speed=+1.0")
Bindings=(Name="Q",Command="MoveDown")
Bindings=(Name="E",Command="MoveUp")
Bindings=(Name="W",Command="MoveForward")
Bindings=(Name="S",Command="MoveBackward")
Bindings=(Name="A",Command="StrafeLeft")
Bindings=(Name="D",Command="StrafeRight")
Bindings=(Name="F",Command="FreezeRendering")
Bindings=(Name="MouseX",Command="Count bXAxis | Axis aMouseX")
Bindings=(Name="MouseY",Command="Count bYAxis | Axis aMouseY")
Bindings=(Name="Left",Command="TurnLeft")
Bindings=(Name="Right",Command="TurnRight")
Bindings=(Name="c",Command="ToggleDebugCamera",Control=False,Shift=False,Alt=True)
Bindings=(Name="LeftShift",Command="MoreSpeed | OnRelease NormalSpeed",Control=False,Shift=False,Alt=False)
;XBox Bindings
Bindings=(Name="XboxTypeS_LeftThumbstick",Command="ToggleDebugCamera")
Bindings=(Name="XboxTypeS_LeftX",Command="Axis aStrafe Speed=1.0 DeadZone=0.3")
Bindings=(Name="XboxTypeS_LeftY",Command="Axis aBaseY Speed=1.0 DeadZone=0.3")
Bindings=(Name="XboxTypeS_RightX",Command="Axis aTurn Speed=1.0 DeadZone=0.2")
Bindings=(Name="XboxTypeS_RightY",Command="Axis aLookup Speed=0.8 DeadZone=0.2")
Bindings=(Name="XboxTypeS_LeftTrigger",Command="MoveDown")
Bindings=(Name="XboxTypeS_RightTrigger",Command="MoveUp")
Bindings=(Name="XboxTypeS_A",Command="SetFreezeRendering")
Bindings=(Name="XboxTypeS_B",Command="MoreSpeed | OnRelease NormalSpeed")
[Editor.EditorViewportInput]
Bindings=(Command="MODE WIDGETMODECYCLE",Name=SpaceBar)
Bindings=(Command="MODE WIDGETCOORDSYSTEMCYCLE",Name=Tilde)
Bindings=(Command="DELETE",Name=Delete)
Bindings=(Command="EDCALLBACK ACTORPROPS",Name=F4)
Bindings=(Command="QUIT_EDITOR",Name=F4,Alt=True)
Bindings=(Command="EDCALLBACK SURFPROPS",Name=F5)
Bindings=(Command="EDCALLBACK LEVELPROPS",Name=F6)
Bindings=(Command="ACTOR SELECT ALL",Name=A,Shift=True)
Bindings=(Command="POLY SELECT MATCHING BRUSH",Name=B,Shift=True)
Bindings=(Command="POLY SELECT ADJACENT COPLANARS",Name=C,Shift=True)
Bindings=(Command="DUPLICATE",Name=D,Shift=True)
Bindings=(Command="ACTOR SELECT MATCHINGSTATICMESH",Name=E,Shift=True)
Bindings=(Command="POLY SELECT ADJACENT FLOORS",Name=F,Shift=True)
Bindings=(Command="POLY SELECT MATCHING GROUPS",Name=G,Shift=True)
Bindings=(Command="POLY SELECT MATCHING ITEMS",Name=I,Shift=True)
Bindings=(Command="POLY SELECT ADJACENT ALL",Name=J,Shift=True)
Bindings=(Command="POLY SELECT MEMORY SET",Name=M,Shift=True)
Bindings=(Command="ACTOR LEVELCURRENT",Name=M)
Bindings=(Command="ACTOR MOVETOCURRENT",Name=M,Control=True)
Bindings=(Command="SELECT NONE",Name=N,Shift=True)
Bindings=(Command="POLY SELECT MEMORY INTERSECT",Name=O,Shift=True)
Bindings=(Command="POLY SELECT REVERSE",Name=Q,Shift=True)
Bindings=(Command="POLY SELECT MEMORY RECALL",Name=R,Shift=True)
Bindings=(Command="POLY SELECT ALL",Name=S,Shift=True)
Bindings=(Command="POLY SELECT MATCHING TEXTURE",Name=T,Shift=True)
Bindings=(Command="POLY SELECT MEMORY UNION",Name=U,Shift=True)
Bindings=(Command="POLY SELECT ADJACENT WALLS",Name=W,Shift=True)
Bindings=(Command="POLY SELECT MEMORY XOR",Name=X,Shift=True)
Bindings=(Command="POLY SELECT ADJACENT SLANTS",Name=Y,Shift=True)
Bindings=(Command="ACTOR SELECT MATCHINGSTATICMESH ALLCLASSES",Name=Z,Shift=True)
Bindings=(Command="EDIT COPY",Name=C,Control=True)
Bindings=(Command="EDIT PASTE",Name=V,Control=True)
Bindings=(Command="DUPLICATE",Name=W,Control=True)
Bindings=(Command="EDIT CUT",Name=X,Control=True)
Bindings=(Command="TRANSACTION REDO",Name=Y,Control=True)
Bindings=(Command="TRANSACTION UNDO",Name=Z,Control=True)
Bindings=(Command="BRUSH ADD",Name=A,Control=True)
Bindings=(Command="BRUSH SUBTRACT",Name=S,Control=True)
Bindings=(Command="BRUSH FROM INTERSECTION",Name=I,Control=True)
Bindings=(Command="BRUSH FROM DEINTERSECTION",Name=D,Control=True)
Bindings=(Command="PREFAB SELECTACTORSINPREFABS",Name=P,Shift=True)
Bindings=(Command="ACTOR ALIGN SNAPTOFLOOR ALIGN=0",Name=End)
Bindings=(Command="ACTOR ALIGN MOVETOGRID",Name=End,Control=True)
Bindings=(Command="CAMERA ALIGN",Name=Home)
Bindings=(Command="CAMERA ALIGN ACTIVEVIEWPORTONLY",Name=Home,Shift=True)
Bindings=(Command="MAP BRUSH GET",Name=P,Control=True)
Bindings=(Command="ACTOR FIND KISMET",Name=K,Control=True)
Bindings=(Command="ACTOR SELECT ALL FROMOBJ",Name=A,Control=True,Shift=True)
Bindings=(Command="ACTOR SYNCBROWSER",Name=B,Control=True)
Bindings=(Command="ACTOR DESELECT",Name=Escape)
Bindings=(Command="CTRLTAB SHIFTDOWN=FALSE",Name=Tab,Control=True)
Bindings=(Command="CTRLTAB SHIFTDOWN=TRUE",Name=Tab,Control=True,Shift=True)
[UnrealEd.ObjectEditorViewportInput]
Bindings=(Command="TRANSACTION REDO",Name=Y,Control=True)
Bindings=(Command="TRANSACTION REDO",Name=Z,Control=True,Shift=True)
Bindings=(Command="TRANSACTION UNDO",Name=Z,Control=True)
[Engine.Console]
ConsoleKey=Tilde
TypeKey=Tab
MaxScrollbackSize=1024
HistoryBot=-1
[Engine.UIInputConfiguration]
AxisEmulationDefinitions=(AxisInputKey=MouseX,AdjacentAxisInputKey=MouseY,bEmulateButtonPress=False)
AxisEmulationDefinitions=(AxisInputKey=MouseY,AdjacentAxisInputKey=MouseX,bEmulateButtonPress=False)
AxisEmulationDefinitions=(AxisInputKey=XboxTypeS_LeftX,AdjacentAxisInputKey=XboxTypeS_LeftY,bEmulateButtonPress=True,InputKeyToEmulate[0]=Gamepad_LeftStick_Right,InputKeyToEmulate[1]=Gamepad_LeftStick_Left)
AxisEmulationDefinitions=(AxisInputKey=XboxTypeS_LeftY,AdjacentAxisInputKey=XboxTypeS_LeftX,bEmulateButtonPress=True,InputKeyToEmulate[0]=Gamepad_LeftStick_Up,InputKeyToEmulate[1]=Gamepad_LeftStick_Down)
AxisEmulationDefinitions=(AxisInputKey=XboxTypeS_RightX,AdjacentAxisInputKey=XboxTypeS_RightY,bEmulateButtonPress=True,InputKeyToEmulate[0]=Gamepad_RightStick_Right,InputKeyToEmulate[1]=Gamepad_RightStick_Left)
AxisEmulationDefinitions=(AxisInputKey=XboxTypeS_RightY,AdjacentAxisInputKey=XboxTypeS_RightX,bEmulateButtonPress=True,InputKeyToEmulate[0]=Gamepad_RightStick_Down,InputKeyToEmulate[1]=Gamepad_RightStick_Up)