Are your USB ports working? Unplug the yoke & rudder and plug them back in and see if that helps. Check in device manager that the USB portas are not disabled.
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Sounds like you need to go into Settings/Controls within FSX and make sure they are assigned to the right axes.
Plugging the devices into different USB ports can be the cause - each port applies a unique identifier in the FSX .cfg for the controller. Plug into a different USB port = different device.
Also check your USB ports themselves are not allowed to hibernate with non-use.