Thunderbolt partitioned and formatted hard drive not recognized on USB2/3

I have a MBA (mid 2012) and recently purchased a Seagate Desktop Thunderbolt Adapter (STAE129), a Seagate Backup Plus 4TB USB 3.0 external drive (STCA4000100), and Apple Thunderbolt cable. The 4TB hard drive can be separated from the USB 3.0 adapter and the drive placed on the Thunderbolt adapter. I created two partitions (3TB and 1 TB) on the 4TB drive while it was mounted on the Thunderbolt adapter and formatted them Mac OS Extended (Journaled) using partition map scheme GPT. Everything works as expected, the drive hits r/w speeds in the 180 MB/s range (using Blackmagic Disk Speed Test), and no issues at all transferring data to the 3TB partition and using the 1TB partition for TimeMachine.
However, if I disconnect the hard drive from the Thunderbolt adapter and place it on the USB 3.0 adapter and connect it to my MBA, Mountain Lion says "The disk you inserted was not readable by this computer and gives me the options to Initialize, Ignore, or Eject. Going into Disk Utility app, the drive shows up without the partitions I created when the same drive was mounted to the Thunderbolt adapter (just shows disk1s1). In fact, the drive label (Disk Description) is different too and the Partition Map Scheme now shows MBR!
To try work-arounds, I went ahead and repeated the partitioning and formatting steps with the drive attached via USB 3.0 and all works fine until I put the drive back on the Thunderbolt adapter where once again OSX reports that the disk is not readable. I've even tried a single partition with no luck. In short, the drive partitioned and formatted on Thunderbolt is unrecognized under USB and vice versa.
Shouldn't the disk preparation and data be consistent across these different interfaces? I would think so. My biggest concern is that if I had a failure in the Thunderbolt setup (assuming the drive itself does not fail), then I can't access my data. This is not a very comfortable situation.
I'm assuming I've overlooked a very basic detail. Appreciate any steer to solve this problem.
Thanks,
Rob

Thanks for that, I recently ran into the same problem. I even chatted with Seagate tech support and they didn't know the answer.
My situation is a bit different from you. I bought the 3 TB Thunderbolt version of the drive directly and then purchased a USB 3 adaptor seperately. You see, I still own a 3 year old Macbook Pro that doesn't come with a Thunderbolt port. I was looking to upgade to a MacBook Air later. I thought that I might as well buy the TB version now.
In anycase, my old MacBook Pro won't see the drive when I use the USB3 adaptor. I get the same exact error message as you did. I can't really test it on Thunderbolt since I don't have one. I'm going to go install the Thunderbolt drivers now and hopefully, it will recognize the drive afterwards. I'll let you know what happens.
BTW, I was thinking of reformatting the drive with NTFS so that I can use the drive on PCs. My mac has the NTFS drivers loaded so it's no problem. I hope this won't screw up the Thunderbolt connection later when I do get the Macbook Air?

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