There's most likely nothing wrong with your stick and pedals, they've just lost their mapping. Your memory serves you right, there's "something that allows you to see the movement".
In game go to Clipboard: Options>Controllers>Map Controllers: Advanced. Do this for every axis you're going to use, map the axis and set the movement range.
The Calibrate Controllers option is a quick and dirty tool to fix existing calibration for correctly mapped controllers. That can be done even during flight as it doesn't affect the autopilot functionality.