Hi Shadow,
I think the problem is the driver that is not seeing the displays properly.
Please plug first through one DP port (native on the vga card) a single display and the other two on the MST hub. Once you boot up the first screen you should see the native port, the other two if you do not see them press the scan button or enable them under display properties. 
Once the screens are visible set one of the displays as your primary display on the MST Hub and then you can proceed to unplug the native DP port cable and place it on the MST.
Check if that works for you.
Also is good to drain your system power before you proceed to set your MST Hub, this is by unplugging your main power cable, press the power button for a few seconds.
Kind regards