In fact there is a known issue with Intel(R) Matrix Storage Manager 8.9. More information is available on the following article:
I suggets you to update to Intel(R) Rapid Storage Technology or use Intel(R) Matrix Storage Manager 8.8 instead and try again.
Last night I updated to the current Intel Rapid Storage Technology via iata_enu_10.8.0.1003.exe. It did not seem to help.
That server, before and after the update, was getting into completely a unresponsive state, even after a couple of reboots. The hdd activity light was on continuously. The only thing that now has it acting somewhat normally is to remove one of the raid disks.
It's a serious problem. The ROM raid is not at the current version. Or could it be that these hard disks (WD3200AAKX) are not very good with raid. I've heard that, but also read that others are using them fine. The motherboard is ASUS P6X58D-E.
To update the option ROM in the system you need to check with motherboard manufacturer who is the one that implements that into your system.
About the hard drives, we do not have a list of tested and compatible hardware for the SATA controllers, you might need to check with the hard drive manufacturer to see if they have validated these drives to be used in RAID configurations and check with them to see if the drives are working fine.
Concerning the rebuild cycle, at this point you might need to back up all the information on the RAID volume, then reset the disks to non RAID. That would leave two separate hard drives with pretty much the same information on each one of them (since the rebuild has not ben completed), then you can create a new RAID 1 array using one of the hard drives as a source (you need to use the option that asks you to save the contents on that drive to preserve the information).