I second this, I thought I was just missing something, but I can't find any info on it, and I want to try to do it right.
I have Western Digital WD20EARS that also have 4K sectors.
I have found numerous mentions of a 4K checkbox on freenas 7 (which I've never used as I am completely new to FreeNAS).
Any help, or guidelines to check that things are aligned properly would be helpful, thanks.