Java always calls the method that best suits your argument. Auto boxing and implicit upcasting is only performed if there’s no method which can be called without casting / auto boxing.
The List interface specifies two remove methods (please note the naming of the arguments):
remove(Object o)
remove(int index)
That means that list.remove(1)
removes the object at position 1 and remove(new Integer(1))
removes the first occurrence of the specified element from this list.