I wrote up a trac ticket and made a patch:
http://trac.sagemath.org/sage_trac/ticket/12385
With my patch, your code snippets evaluate as follows:
sage: Q = DiGraph({1: {2:'a'}, 2: {1: 'b', 3: 'c'}, 3: {2: 'd'}})
sage: Q.all_simple_paths([1], [2])
[[1, 2]]
sage: Q.all_simple_paths([2], [1])
[[2, 1]]
-Keshav
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