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Not quite sure I understood? You mean it's too sensitive?

I've just added a bunch of extra modules for the new Puck.js, as well as one to improve the power usage: http://www.espruino.com/Puck.js#on-board-peripherals

So you can now do:

require("puckjsv2-accel-movement").on();
var idleTimeout;
Puck.on('accel',function(a) {
  LED.set();
  if (idleTimeout) clearTimeout(idleTimeout);
  else print("Motion", a);
  idleTimeout = setTimeout(function() {
    idleTimeout = undefined;
    LED.reset();
  },500);  
});
// turn off with require("puckjsv2-accel-movement").off();

If it's too sensitive, you can do:

require("puckjsv2-accel-movement").on({
  threshold : 20,
});
// ...

The default is 2, so you can just change the value to tweak the sensitivity. There's also a duration option which you can set to ignore short-lived movement.

I've removed the change for now, but it's not working exactly like before. Do I need to reset the register?

Using your original code? You could try just power cycling it?