Is there an update loop or something else that could break my analog readings?

[Testbild-synth]

So I am currently using your library (great work btw) for building a taiko no tatsujin controller using a real drum. For this I read out different analog inputs from piezo sensors in a loop, smooth the values and then apply some thresholding.

If I use the sketch without the joycon library it works fine, but as soon as comment in the joystick commands and send button presses it reacts completely different to the input.
Is there an update loop or something else that could impact my readings (since I do the smoothing, blocking for longer periods of time will also impact them)?