Windows tries to stabilize itself for connections, and when conflicts occur it will dynamically reassign things, but seems to only do so on boot. Depending on hardware, some have reported having to connect things in specific order, but I personally have never seen this. Windows does try to remember device by USB connection, so cycling connections isn't often useful. That being said, simply unplugging/re-plugging in a USB connection can force Windows to re-evaluate itself.
I assume the USB3 port is on the motherboard, and not sure what drivers it is using. You may want to try plugging that into a USB2 port just to check it.
Driver updates for your system may also be contributing. As the machine is new, it is unclear if drivers are up to date for hardware components (the stock drivers in on the Win7 DVD are outdated in most cases).