PROBLEM SOLVED......
I have been having the same issue with my new 3tb Toshiba External connected to My MacBookPro and/or my iMac (tested on both) would dismount when the computer sleeps for 2 hours or more. I was connecting the drive thru a powered usb hub (dlink).
When using the hub the external would eject after 2 to 3 hours of the computer sleeping. When connected directly to the computer the drive would stay mounted after waking my mac/s from sleep. No more annoying message when I wake my mac/s.
I have no choice but to use a hub, as I have many external usb devices. So I needed to swap a few things around to get the external on one of the ports of my mac/s.
Going to system prefs and unchecking putting the hard disk to sleep is only for the internal drive. So this does not work!
Remember: Time Machines function better when connected directly to the mac, do not use a hub (even if it's powered)....