USB ports are usually controlled by motherboard BIOS settings, check there to see if they're in sleep mode or something.
In Windows, your best bet is to identify the ones that work by checking the following information:
Location: Port_#000x.Hub_#000y
Where x and y identify the hub and the port depending on your configuration. The information is listed under the properties of the USB device, and if it does not have that information then it is not a port.