In case it helps anyone...after putting up with this problem for almost a year, I did one final bit of Googling to try to find a solution. And I did solve it, and perhaps it's something that Naslite needs to address in a future update.
I'm far from an expert in hard disk technology, but apparently the problem I was suffering was caused by misaligned partitions. For Advanced Format disks, default settings in fdisk and parted cause misaligned partitions. Or at least they did in the past. I'm not sure if the issue has been addressed in recent builds of the programs. I'll give reading links at the end of this post.
Sure enough, when I took my two 3TB Advanced Format disks out of my Naslite server and stuck them in a Linux box, gdisk (GPT fdisk) reported a problem with the partitions on my disks. So did parted.
Using gdisk I re-partitioned the two disks, and then re-formatted them.
When I put the disks back in the Naslite machine, transfer speeds were transformed -- I'm now getting a steady 30MB/s or so, compared to an average of 8MB/s or so before I re-partitioned the disks.
I started my reading on this informative thread in a media player forum (not all the posts are helpful, but some of them pointed me in the right direction):
http://goo.gl/K6mN4A detailed white paper from IBM which includes information on the performance penalties you can suffer with misaligned partitions on Advanced Format disks (although I seemed to suffer far more severe penalties than those suggested in the paper:
http://www.ibm.com/developerworks/linux/library/l-4kb-sector-disks/gdisk (GPT fdisk) is a helpful tool:
http://www.rodsbooks.com/gdisk/I used PartedMagic as my Linux LiveCD, it contains all the necessary tools:
http://partedmagic.com/EDIT: One problem that still exists from my original posts (if it is a problem) is that system loads still run at 400-450% when writing to the 3TB disks. This compares to 60% approx when writing to other disks. Why would that happen, and what does it mean?