Weird HDD space issue…

The WD Black is SATA2 and the HGST is SATA3.

I guess this is one of those weird anomalies I'll never know the cause to.

The only thing I can think of is the Hitachi uses Advanced Format and the WD does not, does AF affect available storage space?

I would suspect yes.

In a standard format disk the sector size is 512 bytes while with advanced format it becomes 4096 bytes, the same size as a standard cluster. Thus, advanced format shouldn't effect file storage efficiency. But the NTFS metadata, data used by the file system itself, may well be effected. Much of the internal operation of NTFS has never been been publicly documented.

Britton30 said:

IT shouldn't make a difference but I wonder how they'd read if connected to your motherboard? On the correct SATA II or SATA III ports.
This is just a WAG (wild-ass guess) that the two SATA interfaces read bits and bytes differently.

PATA, SATA, SAS are all controllers and SATA I-III are different generations of the same controller. I haven't seen evidence indicating that one controller would write more data to disk than the other when writing a file of the exact same size.

LMiller7 said:

I would suspect yes.

In a standard format disk the sector size is 512 bytes while with advanced format it becomes 4096 bytes, the same size as a standard cluster. Thus, advanced format shouldn't effect file storage efficiency. But the NTFS metadata, data used by the file system itself, may well be effected. Much of the internal operation of NTFS has never been been publicly documented.

That was my initial impression because I remember reading a long article when Advanced Format was introduced. There was something about how NTFS interprets Legacy vs AF architecture but I forgot if that had anything to do with how data is written to the drive.

TVeblen said:

Another suggestion would be to use Partition Wizard (you can use the bootable CD if you don't need/want to install it on your system). See if it reports unallocated space that Windows does not report.
Free download Magic Partition Manager Software, partition magic alternative, free partition magic, partition magic Windows 7 and server partition software - Partition Wizard Online

I don't think that would be the case because initially the difference was 1.05GiB. After I deleted the Hitachi volume and quick formatted the drive and copied the data over again from the WD the difference is now 40.2MB.

Like what LMiller7 said, the difference could just be metadata left over on the WD drive since that drive is a 2009 drive while the Hitachi is a 2012 drive and Advanced Format did not hit the market until 2010.

Britton30 said:

No Offense, but thinking something is so doesn't make it so. Testing as TVeblen or swapping controllers in a PC as I suggested may or may not shed a light.

None taken and you may be right, but if a specific type or generation controller caused more data to be written wouldn't there be articles all over the web indicating such issues? I think people would be up in arms if a certain controller caused more data to be written than normally should.

eSATA is currently connected to a Marvell controller, I'm going to connect it to the Intel 6Gb/s (Z68) and see if that makes any difference.

Thinking back, I forgot to mention the EX-503 enclosure was initially connected via USB 3.0 (Renesas controller) and I switched to eSATA because transferring files over USB 3.0 would cause folders I was opening on the external to lock up, but the transfer would still continue in the background and transfer speed was awfully slow (~26MB/s).

This new enclosure is giving me a lot headaches.

When I first got my EX-503 I popped the back open to replace the stock fan with a quieter 140mm fan. I noticed the board was just a plain jane eSATA to USB 3.0 board but I decided to connect it via USB 3.0 anyway because I wanted to keep all the cables in the back and I knew the 2x eSATA ports in the back were crappy jmicron ports (I just didn't know how crappy).

When connected through USB 3.0 I would get lock ups and BSODs that's when I had to switch to eSATA. I started with the eSATA the ports in the back (P8Z68 Deluxe) and that's when I found out what garbage of a controller jmicron is on this mobo. It's worse than Marvell's controller and I was pulling around ~30MB/s on sustained transfers. Then I switched to the front eSATA port (Marvell) sustained speeds improved a little but not by much ~55MB/s.

Finally I switched the front eSATA to Intel's 6Gbps port (I know 3/6Gbps doesn't make a difference for HDDs and I only have 1 disk that requires 6Gbps anyway, my 256GB Vector) speeds were around 80MB/s sustained, but still slow ass heck when moving around 2TB of data.

I might just end up getting a dedicated eSATA card because I really want to keep all the cables in the back but I think a good card runs around $300.