no, 1&3 or 2&3 haven't seemed to matter. they both give dual channel. in terms of performance, some people *claim* that they get better oc ability from 1&3 vs the manual's recommendation of 2&3, but, those cases are far and few between.
as reference, i use 1&3 (i tried 2&3, but got same results) only so that there's more space in between the two sticks for "better" airflow (better in quotes, because clearly it's hardly significant).