There is no point in running CHKDSK now that you have repartitioned and reformatted your drive. Had you run it before, I suspect it would have complained of read errors beyond the 1TB limit. Moreover, since the original MBR has been rewritten, we can no longer examine the old partition table.
As for HD Tune’s Info tab, it doesn’t show the information I was looking for. In particular I was looking for the model number of the HDD, eg WD20NPVT or WD20NMVW (perhaps the drive doesn’t report this?). Do other utilities, eg HD Sentinel, show this information?
Could we see HD Tune’s read benchmark graph? This will tell us if the drive has been short-stroked, which will in turn support the HPA hypothesis. You will need to achieve USB 3.0 transfer speeds for this benchmark to be useful, otherwise we will only see a flat line.
The ATA standard provides a READ NATIVE MAX ADDRESS command that can detect the drive’s full native capacity. However, I don’t know which utilities, if any, are able to retrieve this information from the drive via USB. Perhaps hdparm can do this?
BTW, I still can’t see 20120808143515.jpg.