Version 4.1, like all previous ones, still uses a weird ID scheme and it can be a bit confusing when the miner's GPU 0 is Afterburner's GPU 3 or something like that.
Check my explanations:
https://bitcointalk.org/index.php?topic=1433925.msg14659010;topicseen#msg14659010So there is no way to fix GPUs order automatically, thanks to AMD devs.
But you can do it manually. For example, if you have two cards, you can change their order by adding "-di 10". Another example, reverse order for six cards: "-di 543210".