Still didn't work. I attached a screenshot of my RAID utility screen for more information.
Just a note -- The 1TB drive is showing up as a non-RAID disk, exactly what you want. When you set your SATA controller to RAID, then all drives connected will come up under the RAID listing because they can all
potentially be used as RAID disks. You can see that the two 500GB drives are RAID array members, while the 1TB is non-raid.
As for your boot issue - it still sounds like a BIOS setting is incorrect. It sounds like the computer is trying to boot from the 1TB drive first. Did you go in the BIOS and make sure to set the RAID array as the first priority to boot from?
You can also try hitting "F8" when the computer boots (or F12, some BIOSES set this function to F12) to get a list of boot drives. Do this right when the BIOS screen comes up. When the list of drives comes up, select your 500GB drive/array. See if that works.
If it gets into Windows, then the 500GB array hasn't been selected properly in the BIOS as the boot drive(s), since it works when you force them to be the boot drives, but is probably defaulting to the 1TB drive otherwise.
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Another solution is to use the 1TB drive in a USB 2.0/3.0 or eSATA enclosure. Then you can connect or disconnect the drive whenever you want. USB 2.0 maxes out at about 20-30MB/s, so if performance is an issue then this solution isn't ideal.