I don't own your board, so cannot give you any direct experience. I don't recall seeing this issue posted in the forum as long as I've been hanging out here (~9 months), but your board is certainly not mainstream or common.
I'm surprised the Samsung 840 Pro SSDs did not work with the LSI RAID controller, but there have been a few reports I've seen in other forums/websites about RAID issues with those Samsung SSDs, and that was on the Intel RAID controller.
The Intel RAID 1 results with the Agility 3's is great, better than I would have guessed for that SSD.
You may have seen this thread elsewhere, but just in case you haven't, similar issues to yours: Interesting Windows Server 2012 LSI SAS2308 Controller Results
Frankly, IMO ASRock support will not have much experience with the LSI RAID controller, so they won't be much help. Was LSI helpful, or just passed the buck to ASRock?
I imagine you've been through this, but just in case, when you installed Windows (what version?) did you install the so called LSI Floppy Image ver:2.00.55 driver? The download file expands into four versions, two for AMD and two for Intel. Each folder has a text file that describes the installation, etc. You may find some information in that documentation htat