I had a similar problem this week. I caulk it up to inexperience on the new chasis. Weasel5053 is correct, you have to make sure that your system is fully up and running on the first hard drive on the non-RAID board before adding in the RAID controller and the 2nd hard drive.
Also, if you add the RAID controller and think that the 1st hard drive is a problem and then put another in that place, the replacement will not work. This is because the RAID card will take registration data from the first drive. To clear the registries, turn off the system, unplug all hard drives, turn on power for 10 - 20 secs and then off again. Plug in the 1st hard drive and it should be good to go.
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My Biggest problem is that I almost always believe what I tell myself.