Did you ever have a chance to try hooking the 3008 directly to the SATA drives with the new cable? I'm looking to pull the trigger on the same board, but initially, will not need the LSI expander. I will just use SFF-8642 to SATA cables until I add more drives and pick up another expander.
Yes I did actually, I ran into the same problem unless I switch from FN to Linux. I tried loading FreebSD, I tried loading NAS4Free, both had the very same issue, but when I load Ubuntu or Gentoo, the problem goes away completely. In any case, since there are several other people running that same board without any issues, I decided to go ahead and put test data on the box and test performance even though it looked like there may be an issue. Long story short, I can completely saturate 2Gbps of a 10G link (tested with iperf to 6+Gbps) on reads and as high as 5Gbps (tested with iperf to 9.41Gbps) on writes. Now, mind you this was with nfs and a single 12 Drive vdev RAIDZ2. I have since moved to 2 x 6 Drive VDEVS RAIDZ2. I suspect I will see better performance, but I have not tested it as of yet.
You can read about this performance testing and my attempt to speed up NFS
HERE.
So in the end, even with a perceived performance issue when doing DDs directly to the /dev/da device, with 2 vdevs in RAIDZ2 with sata drives, this motherboard absolutely rocks. If you were not going to run 10G, then this board will completely saturate a gig link each direction all day long.