tanik1,
You are the first person I've seen that had SMART work with Highpoint.. LOL! Count yourself lucky! I just might have to pull out my 4520 and try it again for good measure. Damn you!!!
As for the 4k thing, FreeBSD 9 has a blacklist of hard drives that lie about their sector size.
You can check your vdevs by querying the ashift value(zdb -C <yourzpoolname> | grep ashift). The ashift is the power of 2, so 9 = 512bytes and 12=4k. In FreeNAS 9 it "should" be smart enough to get it right. If it doesn't, you don't really have any choice except to do it from the command line. I put in a ticket for this issue already with FreeNAS 9.
http://support.freenas.org/ticket/2404. Hopefully it will make it into the next version of FreeNAS.
My issue, if you read that ticket, is that I want the option of forcing 4k even if I'm using 512bytes per sector disks because I want some forward thinking options. I also question how complete the blacklist is and I'd hate to be that sucker that happens to not be on the blacklist. Ashifts can't be changed once the vdev is created. So you have to choose wisely.
As far as I know you can't clear the self test log. That's stored on the hard drive itself and I've never seen any option to clear it. My drives keep the most recent 100(or 20 for some of my drives) test results. I know if I connect to the controller's serial port and issue commands to the drive I can wipe(or change) any raw SMART parameter that I want. But it's not something I'd ever recommend anyone do, especially if you haven't done it before. You can permanently damage a hard drive if you aren't very careful.
Drk,
If you run the ashift command I mentioned above you can see if your zpool is aligned to 512 bytes or 4k sectors.
If you have a 4k drive with a 512 byte alignment, the performance penalty can vary from 1-5% to 40% or more depending on your work load. If you have a 512 byte drive with 4k alignment you have a performance loss of 5-10% and you lose some disk space due to the wrong alignment. Those numbers are off the top of my head, so I may have them wrong.
Personally, I always choose 4k right off the bat just to be "future proof".