Well, it is possible that the USB ports that aren't working are a different version (3.0/2.0) than the one that is working.
I would check for any driver updates, and if there are any, install them.
After that, try the following and see if it fixes it.
1. Go to "Control Panel" and then "Device Manager".
2. Expand the "Universal Serial Bus controllers" section.
3. Double-click on the "USB Root Hub device".
4. Now click the "Power Management" tab.
5. Uncheck the "Allow the computer to turn off this device to save power" option.
6. Click the "OK" button.
NOTE: If there is more than one "USB Root Hub device" listed, Then you will have to repeat this steps for each one of them.
7. Restart the computer and all the ports should work now.