I am extra careful about connecting the cables correctly. I have tried all possible combinations, I even made a USB cable to connect the Aquaeros to the external USB connectors of the motherboard: A type connector on one side and 1x5 internal USB connector on the other. Cables work perfectly but the problem persists. Its very strange and only happens at boot time if both Aquaeros are connected. If I connect the second Aquaero once Windows has booted, both Aquaeros are properly "mounted" and Aquasuite runs perfectly.
Mobo is Asus Rampage II Gene, I7 920, Windows 7 64bit (same behaviour with Vista 64bit)