Conemaugh,
Whats happening is every time you even just open the options/controls in game, the refuel mod and the reece mod entries get erased. Quirk of the game. You have to reinstall those entries in the controls INI that you are using. Open the controls folder and check the INI you are using and make sure these entries are there. If you change the mapping for them on your stick or keyboard, you have to go back into the INI and add them again.
//at the end of controlset001
PITCH_TRIM_CONTROL=
ANIMATION_1=CTRL+1
ANIMATION_2=CTRL+2
ANIMATION_3=CTRL+3
ANIMATION_4=CTRL+4
ANIMATION_5=CTRL+5
ANIMATION_6=CTRL+6
ANIMATION_7=CTRL+7
ANIMATION_8=CTRL+8
ANIMATION_9=CTRL+9
ANIMATION_10=CTRL+0
GOTO_CAMERA_LEFT_VIEW=NUMPAD1
GOTO_CAMERA_RIGHT_VIEW=NUMPAD3
GOTO_CAMERA_DOWN_VIEW=NUMPAD2
GOTO_CAMERA_FRONT_VIEW=NUMPAD5
//at the bottom of the ini
[RangedControl009]
AxisControl=PITCH_TRIM_CONTROL
MaxValue=1000.000000
MinValue=0.000000
DeadZone=5.000000
Saturation=75.000000
ReverseJoystick=TRUE
MouseScale=1.000000
UseMouseRate=FALSE
ReverseMouse=FALSE
LimitValue=TRUE
SelfCenterRate=0.000000
KeyControlRate=1.000000
AllowKeyControl=TRUE
IncreaseControl=THRUST_VECTOR_UP
DecreaseControl=THRUST_VECTOR_DOWN
CenterControl=
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