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

I disabled "power nap" and this has completely solved the problem for me. I've been through 3-4 sleep/wake cycles and not one problem. Previously, I had it every sleep/wake cycle.

For me, I don't care at all about the power nap feature, so I'm good. It is very, very disappointing that Apple's software quality is gone down so much, though.

I had the disk not ejected properly problem since 10.7. I have a mid 2011 21.5 inch iMac. The problem continued after installing El Capitan, but I have finally found a solution that works. I installed Mountain to unmount the external drive when when the mac goes to sleep, and remount the drive when the mac is wakened. That solved the problem from happening when the mac was sleeping, but the problem persisted at random intervals while using the computer. This was caused by the external drive going to sleep on its own and ignoring the unchecked "put hard drives to sleep" in system preferences. Apparently many external drives do this. To solve this problem I installed "Keep Drive Spinning", which you can set to access the drive at any interval you wish to keep it froim going asleep. I set mine to 540 seconds (9 Minutes) because many drives go to sleep after not be accessed for 10 minutes. These fixes have completely solved the problem.

Mountain: https://itunes.apple.com/us/app/mountain/id528726140?mt=12http://www.macupdate.com/app/mac/43428/mountain

Keep Drive Spinning: http://www.macupdate.com/app/mac/31158/keep-drive-spinning

Spoke too soon. This problem persists with both Mountain and Keep Drive Spinning installed...

Have you tried turning off "power nap"? That worked for me.

I've searched this whole thread, but I don't see this option listed.

I had this happening, too. It was after upgrading to El Cap. However, I seem to remember it happening with Mavericks, too.

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!

"Power Nap" doesn't exist on iMacs - it's only for laptops. May try formatting the drive, but need to research whether it has done any good for others with this problem.

Same here with my brand new MBP with El Capitan. I don't know if this is a clue or not but I was using the Thunderbolt connection with Firewire to my external drive when this kept happening. Over last two days I switched to the USB 3 connection and so far no error messages and seems to be staying mounted.

Update: after reading many posts mentioning that problems were happening with firewire and USB 3 connections, I tried switching my G-Drive mobile to its USB 2 port instead of the firewire port. This seems to have solved the problem. At the very least, it has reduced the frequency of the DNEP warnings (it has never happened since the switch, but you never know). I should add a reminder that this is with Mountain and Keep Drive Spinning installed....

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?