You didn't really answer many of my questions. I'm trying to help you diagnose this, but can't really help if you won't try these things. As I explained, not all of these benches produce apples to apples comparable numbers (especially on SF drives) and what you are seeing is probably correct/normal for the hardware you are using.
That said, I doubt that your controller is crapping out on you. The "onboard raid controller" is the same hardware as the non-raid onboard controller and, as F@32 mentioned, software raid is sometimes faster than hardware raid (hardware being used loosely in this case since its just an alternate implentation of software raid in this case).
--Matt
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