A PC without an OS, or an OS just being installed has virtually no drivers, so most things won't work, no surprise really. That includes the USB 3.0 ports.
Use the USB 2.0 ports on the boards I/O panel for installing Windows from a USB flash drive, that has always worked for me.
I guess the "2 x Ready-to-Use USB 3.0 Ports" on the I/O panel are not really ready. Or your version of Windows does not have drivers for those USB 3.0 ports.