Q: "Disk Not Ejected Properly" error after EL Capitan goes to sleep and wakes up again.

So then do we have a hardware or software defect involving the thunderbolt ports?? I sure would like to know since I just bought this new MBP.

My new imac have Power Nap. All new relatively new iMacs have it. I believe all relatively new Macs - all of them - have it. It's OSX standard now.

My guess is that it is a OSX bug and hopefully it will be fixed by Apple. It's all a lottery.

This was a constant problem for me through the last two versions of software. I leave my machine on almost all the time and often have safari open. Two weeks ago I switched to Chrome as my browser and the problem has not occurred since. I had disabled spotlight search from al my external drives and that had none nothing. I hope this helps some of you. If it should recur I will post that.

I'm still having this problem on a Mid-2012 MacBook Pro with Mac OS X 10.11.4 and an external USB 3.0 G-Drive. Has anyone discovered a solution?

I have the same problem with OS X 10.11.4.  My thunderbolt WD dou suddenly keeps ejecting then reappearing.  I get the message "Disk not ejected properly" several times over night.  Anyone found a solution?

I did not have this problem before until I upgraded to 10.11.4 on my 2015 15" MBP attached to my TimeMachine drive (USB3 WD 1TB MyPassport).  I tried resetting the SMC but it did not help.

The only solution I found was to set computer sleep to never.

I think the workaround (option) that worked for me was --  System Preferences, Security & Privacy, General, Click on Advanced - You might need Admin password at this point.  Inside Advanced, I had to make sure Log Out After ___ Minutes is UNCHECKED.  I've seen others that were able to set it at a certain time, and they said that worked.  For me, I had to UNCHECK the box.

Maybe this will help someone...It's worth a shot!

The problem is not specific to El Capitan. I'm on Yosemite and it happens to me. I have all my drives hidden from Spotlight. I have Time Machine turned off. I have my energy saver preferences all turned off. I have 6 or 7 usb 3.0 drives connected to powered hubs.

Whenever I turn on my program Cubase (a music production program) it disconnects all of my drives, not just one, ALL! and then Cubase crashes, and all of a sudden my mac is super slow.

I'm on a 2013 Mac Pro.

This is absolutely insane! There is no fix for this. I am going to return my Mac Pro and move to Windows because Apple is a terrible company and my work station has become inoperable.

I discovered a solution that works for my Early 2009 Mac Pro with a USB 3.0 dual hd dock whose drives would go to sleep even while disk utility was repairing them.

I came across Keep Drive Spinning.app, a free utility available at http://jon.stovell.info/software/

It allows a user to set specific lengths of time a drive will be kept awake -- a solution that instantly cured the early sleep problem I'd had.

btw, fwiw, the problem occurred in Yosemite as well, but it has never occurred with drives attached via USB 3.0 in Sans Digital enclosures.

Thank you so much Myaka. I will give it a try, hoping for the best!

While I appreciate the suggestions that Myaka and others have made, I'm really appalled that this problem still persists. I really wish Apple would fix this–and soon.

I have an external G-Drive connected to a MacBook Pro Mid 2012 via USB 3.0. It's also exhibiting the same symptoms everyone else is describing. In speaking with G-Technology tech support, I was told this condition doesn't affect every external drive, such as my WD MyPassport. Although G-Technology is familiar with Keep Drive Spinning, they recommended a paid app called Disksomnia. I just reached out to the developer of Disksomnia to see if his app would solve this issue and I await his response. I'll update this thread as soon as I've heard back. Hopefully, we can put this ongoing problem to bed soon.

Okay, I just tried a tip from Louie at G-Technology. Louie said that if you manually sleep your Mac you will not have a problem with it disconnecting abruptly, which triggers the message, "Disk Not Ejected Properly." I just tried this and it appears he was right. From what I what I was told, this condition ONLY occurs when a Mac goes to sleep on its own. Hopefully, this info is helpful to other users.