Getting Rid Of Disk Not Ejected Properly Message

I've read through the thread but don't remember or didn't see where and when the message is showing. Does the message appear when the computer starts restarting (as in exiting OS X)? When you are using Finder and eject the disks, then pull out the SATA cord(s) immediately after the disk icons disappear from Finder, do you also get a "unsafe ejection" message?

I would try to single out whether the problem originates from the computer or from the drives. Using a different drive with the same port, does the issue happen?

Perhaps the eSATA bus needs more time to eject the drives than RESTART is giving them. Maybe you could use an Automator script that ejects the drives then pauses for XX seconds before restarting the system, giving the eSATA bus more time to eject the drives?
 
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I do not have another eSATA external drive. The problem does not occur with my eSATA internal drives. Problem does not appear to happen with 10.6.8 or 10.8.5. (I have lots of partitions on my internal drives.) NewerTec now owned by OWC does not have a clue.
 
I have tried ejecting the disk before restarting and tried unmounting the disk before restarting to no effect.
 
I do not have another eSATA external drive. The problem does not occur with my eSATA internal drives. Problem does not appear to happen with 10.6.8 or 10.8.5. (I have lots of partitions on my internal drives.) NewerTec now owned by OWC does not have a clue.
Looks like you can get this to work better without more assistance from NewerTech, or OWC.
Do each step. Continue to the next step if the first doesn't change anything.
Step 1: Try a different cable to the eSATA drive.
Step 2: Reseat, then replace the PCIe card.
Step 3: Replace the external eSATA drive.
 
I have tried step 2 to no effect. The drive is a OWC drive so I would have to go back to them. Getting another eSATA cable seems to be difficult in Rochester NY. No one carries them.
 
"One thing I noticed is that the messages appear anytime I wake the computer up from sleep."
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Which would tell me that the system is not giving the drives enough time to before it starts sleeping, and thus is telling you that the drives were not ejected properly.

Since you've verified that this does not happen with other versions of OS X, I would conclude that it isn't a hardware issue.

If you don't want to manually eject the drives before restarting, then perhaps you can make an automator script that does it, pauses for a certain amount of time, and then restarts the system all in one execution. For that, you need to determine whether the eSATA connections need more time before restarting or if OS X just isn't properly letting go of the drives prior to restarting no matter how long you give it to eject the drives. If it isn't properly letting go of the drives, then I'm afraid there's nothing left you can do about that issue. This is why I suggested that you eject the drives in Finder then pull the cable from the computer that the drives are connected with, to determine how long (through trial and error) you'll have to wait before the drives are fully ejected properly.
 
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