Well, Win7 and Vista both apparently Do The Right Thing by default, or so they say.

Many Linux distros still do the wrong alignment by default -- putting partition 1 at sector 63 rather than sector number 64 (65th sector). I don't know what your QNAP does, but probably the same.

Blame WD for some of that -- there's a standard way for the drive to inform the O/S of correct alignment, and the beta versions of these drives did that correctly, but somehow it got lost when they went to production.

There's a jumper on the drive to have it internally offset everything by 512 bytes, for use with appliances like QNAP.

Oh.. and scratch the variable spin speed thought -- these drives are actually fixed at 5400rpm, despite WD's marketing lingo.