Casteil the Issue is prior to Windows the Bios is in charge of the cards and it assigns the top card as primary which 99% of users attach the monitor to. In Windows you can choose the primary card through the drivers. It would need a bios update to change this to allow you to be able to make the second card primary as this is a feature currently not available.
Thanks. it is more of an annoyance rather than anything else. One other question, not related to this thread really, but I have just bought 2 GT1850 fans to replace the stock ones on a H100i, what is the best way to control them as the corsair link is useless with 3pin fans.