At least I think it's the dock. I recently purchased the Elgato Thunderbolt dock so that I could use my USB 3.0 external drive with my rMBP and only have to plug and unplug one cable. My setup is late 2013 15" rMBP to Thunderbolt display then from the TB display to the Elgato dock. I have the external drive plugged into the dock from there. My problem is that when I have the rMBP plugged in and it goes to sleep when I wake up it gives me a warning that the disk wasn't ejected properly. I then have to unplug the drive and plug it back in to initialize it again. I set the drive to never go to sleep in the energy saving settings but it still happens. Any suggestions on how to keep this from happening? When the MacBook is plugged in I really don't want it to go to sleep at all but there's not option for that.