I found this in FlxGamepad.hx, which might help steer you in the right direction -
public function getYAxis(AxisID:Int):Float
{
var axisValue = getAxisValue(AxisID);
// the y axis is inverted on the Xbox gamepad in flash for some reason - but not in Chrome!
// WARNING: this causes unnecessary string allocations - we should remove this hack when possible.
#if flash
if ((_device != null) && _device.enabled && (_device.name.indexOf("Xbox") != -1) &&
(Capabilities.manufacturer != "Google Pepper"))
{
axisValue = -axisValue;
}
#end
return axisValue;