Hi Josh90301 ;
I'm not sure if the problem could be more related to the OS than to the board, I saw different issues about USB ports on Windows Server.
Connected USB device is not detected in Windows
USB devices stop working in Windows 8 or Windows Server 2012
Take a look at that just to discard that the issue is with the OS.
Also, have you tried to boot the board using a SDcard? and, are you using USB2.0 or 3.0?
Regards;
CMata