I was doing a sector by sector scan of my WD My Passport SE 1TB /w USB 3.0 interface, which I only bought last month.
Surprisingly, I couldn't complete it because I didn't have an expandable page file and it swamped this system. Check this screenshot of Chkdsk.exe using 11GB of RAM, before it had to be shut down. Is this is an anomaly due to the drive's hardware encryption or firmware? Possibly.
WD Smartware does have its own diagnostics, including a 'full drive diagnostic' that presumably does a sector by sector check. This does seem to behave fine on the drive, so I suppose the warning here is don't use chkdsk with this model of drive - at least not with the 'firmware' and/or driver versions I was testing with.