This has been bothering me for a long time. I have both a USB3 external hard drive and thumb drive and since updating to windows 8.1, they have not been working correctly. The external hard drive does not work at all on the USB 3.0 port and the thumb drive is very slow.  I have been doing a lot of research and trying many of the suggestions provided, but nothing seemed to work.  Then yesterday, finally found the solution to the slow USB 3 port.  Change the power saving setting in the Control panel.  The following was a post for the Thinkpad T430, so I guess this is fix for anything using the same hardward as the T430 and the Yoga13 Ideapad.

The “USB selective suspends settings” option in the Power Options may be Enabled.

• Click Start, type Power Options in the Search box and then click Power Options from the returned list
• Click Change plan settings for the selected Power plan
• Click Change advanced power settings
• Expand USB settings and then USB selective suspend setting and change the setting to Disabled for the option for On battery: or Plugged in:
• Click OK on the Power Settings window and click Save changes on the Edit Plan Settings window

  Important: This is a default power setting , disabling this setting will cause additional battery power consumption when your mobile PC is in Sleep or Hibernation mode and unplugged.

I recommend that you only do this for the plugged in setting.  If you are on battery, you may want to keep this enabled unless you need the higher speeds.  If so, you can turn it off, pull or push the files you need, then turn power saving back on.  Good luck!