OK, I have been doing some experiments and have not had a disconnection for a couple days. It appears (for me at least) as the trigger for the "DID NOT EJECT PROPERLY" event is when the Mac goes to sleep. I suspect it may be a combination of factors which I have not deciphered yet, including 1) Sleeping, 2) HHD, 3) TimeMachineBackup, and possibly marginal hardware.
By setting Energy Saver settings as follows and not manually entering sleep I have avoided the Disconnect for a couple days where it was reliably occurring at least once a day.
Can someone please try this and tell us if this works for you.
I am on an iMac where battery is not an issue so staying awake just wastes energy. This will have a more significant impact on Laptop users trying to conserve battery.
I have opened a Bug Report but it would be nice if Apple would at least acknowledge this is an issue that will be fixed. Apple?