sum([a, b, c], d) produces d + a + b + c.
In your example, a, b, c, and d are [1, 2], [3, 4], [5, 6], and [].
sum([[1, 2], [3, 4], [5, 6]], []) produces [] + [1, 2] + [3, 4] + [5, 6], which is [1, 2, 3, 4, 5, 6] because + is concatenation for lists.
This is absurdly inefficient, because every + operation involved requires copying all the data from each of its arguments:
In [7]: x = [[i] for i in range(30000)]
In [8]: %timeit sum(x, [])
1 loop, best of 3: 2.06 s per loop
In [9]: %timeit [elem for sublist in x for elem in sublist]
1000 loops, best of 3: 1.91 ms per loop
sum(x, []) takes quadratic time, whereas a more efficient implementation takes linear time. Never do sum(x, []).