From the MSI download page have you installed all the other drivers, including the Intel Chipset?
You can try to run an Ubuntu LiveCD to test the USB ports in a different OS. Ubuntu also has USB3 drivers and it should work right away. DOwnload the image here:http://www.ubuntu.com/download/desktop
and insert a blank dvd then right-click the downloaded .iso file and burn image to the DVD. Boot from it, then select "try ubuntu" when asked for a choice to try or install. Plug in a flash drive to test the ports there when the Ubuntu desktop has loaded. If it doesn't pop up on the screen click the file manager icon on the left hand tray to see it appears in the system there.
If you don't have a blank DVD there are instructions to create a bootable USB here http://www.ubuntu.com/download/desktop/create-a-usb-stick-on-windows