One thing to check might be some of the bios settings. Some systems have a fast boot type of operation that may not initially start some USB ports and other items. If your system has such a setting, you might try turning it off. Also check the settings for the USB and see what is enabled, such as EHCI (not completely sure about the exact letters) to see if it is enabled or disabled.
In Device Manager (devmgmt.msc) you might compare the entry for and the properties of the xHCI Root Hubs and the eXtensible Host controllers to see if they might be present or different when the 3.0 is active. Make sure and check the Properties-Driver-Driver Details to see what drivers are loaded.
How are you removing the drive, with the Safe Removal...