My contributions to the discussion :
Configs:
1. 2013 New Mac Pro - base model quad etc.... no modifications
2. 2012 Macbook Pro Retina 17" - quad, SSD internal, etc...
3. 2012 Mac Pro - 6 core 3.33 internal pci SSD + Sata drives, etc...
4. 2010 Mac Pro - 12 core 2.8 - SSD + Sata internal drives...
External drives:
A. Thunderbolt - G|Drive Pro Thunderbolt 4TB
B. USB 3 - Lacie Rugged 500GB
C. USB 3 - Seagate Expansion 1TB
D. USB 3 + eSata - Comkia (generic) enclosure w/ 500GB Samsung SSD
E. USB 2 + eSata - Vantec Nexstar dock (currently contains a 3TB Seagate 7200rpm Sata drive
... Plus others
OS
All computers are currently running 10.9.2
Successes
#3 and #4 computers above do not exhibit any problems with drives improperly disconnecting. Both computers are either always on or manually powered down. Sleep is not allowed and hard drives are never turned off for energy purposes. Drives B thru E work with no issues (Drive A is Thunderbolt and there is no Thunderbolt port on the old Mac Pros).
Failures
#1 - the new Mac Pro is how this problem was discovered. Purchased August 25, I was told by Apple Care that the problem was the logic board. I returned and exchanged the computer on September 25th at a retail store. Their Genius Bar "confirmed" that it was a logic board problem. Within minutes of setting up the new computer, the "disk improperly ejected" message appeared. I was about to RMA the drive when I decided to try every drive/computer/connection combination to find a pattern.
Here's the track record so far:
1 + A : DNEP when waking. DNEP also during use, at random times.
1 + B : DNEP during use
1 + C : DNEP during waking and during use
1 + D : DNEP during waking
1 + E : Working fine for 4 days. No problems
#2 - 2012 Macbook Pro Retina - I decided to plug the Thunderbolt drive into this computer just to troubleshoot and lo' and behold, the DNEP error message displayed after waking the computer. I was starting to think it was just the drive itself causing the problem, but in the same moment, two USB3 drives failed on the nMac Pro, ruling out the possibility that the problem was computer or hard drive hardware related.
2 + A : DNEP during waking
2 + B : Works fine, only DNEP message was when plugged into a cheap USB3 hub
2 + C : Works fine
2 + D : Works fine
2 + E : Never tested
Next Steps
Just got off the phone with Apple Care tier 1. He's flabbergasted as to why the problem would persist on a separate computer, as his initial thought was the drive was the culprit. He had me update to 10.9.5, and reset the P-RAM. He wants me to call tier 2 if the problem persists. He did not mention anything about cables, power supplies, or energy saving.. but he did spend a lot of time discussing how ports could be bad on the computer.
Based on the messages in this forum I am convinced the problem cannot be a cable problem. How likely is it that all of us would have a bad cable? My cables are new because all of my equipment is new. I am with those who think it's a software problem. Specifically, how the software interprets information coming from the hardware. Neither of my older Mac Pro's have issues connecting to and disconnecting from drives, and none of my drives exhibited issues with improperly disconnecting until the purchase of the new Mac Pro. The same software is installed on all systems but maybe something in the software is interpreting the drive information differently based on the hardware configuration of the computer.
I'll keep you posted with the status of the 10.9.5 update + P-RAM reset