In looking into this to get more information for you, I ended up solving the issue.
My BIOS was set to AHCI rather than RAID, which was intentional -- with SATA mode set to RAID, the BIOS would show the RAID volume info correctly, but it wouldn't make either volume available as a boot option. So I booted in AHCI, and after installing the Intel RST driver, the RAID volume worked just fine anyway. Except that it didn't show up in the Intel RST software.
What I suspect happened is that Windows was managing the RAID array (which was created with ICH9R) as a software RAID array. I'm not sure about this, and I'm surprised that Win7 could manage an array in software that was created with Intel chipset RAID, but it's my best guess. I also don't know why this would cause the volume to not appear at all in the Intel RST software -- that seems like a bug. That's all speculation, though.
What I did to fix the issue was:
- Install a BIOS update, from Asus Z97-A BIOS 0604 (less than a month old) to 1008. This fixes the issue of the hard drives being unavailable as boot options when SATA mode is set to RAID.
- Update the registry to change HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\iaStorV\Start from 3 to 0 (so Win7 doesn't bluescreen when booting with SATA mode as RAID).
- Change the SATA mode in BIOS from AHCI to RAID.
- After booting with SATA as RAID, reinstall Intel RST (setupRST.exe). It would fail with an error on launch before the reinstall.
The only visible change from all that is that the RAID volume now shows up in the Intel RST software -- it looks identical in Device Manager -- but I suspect it changed from software to chipset (Z97) control. Also, Intel RST says "Your system is functioning normally," and it never went through a rebuild or anything. So I don't know what the original "Your system is reporting one or more events, and data may be at risk" was about.