Just in case anyone has the same issue, I had serious compatability problems with this setup upon upgrading from Intel Matrix Storage Manager 8.8 to IRST 9.5. The system would randomly start to consume all CPU and become unusable. Downgrading resolved the issue.
As this was on an ASUS P5Q, Intel has directed me to ASUS for this problem. They said they have no bug reports of any similar issue, but they didn't take a bug report from me either so perhaps that is why. I'm really unimpressed with Intel support right now. I can understand them directing me to my manufacturer, but I am shocked at their failure to take a bug report in case this issue appears in other configurations.
I have reported the issue to ASUS and will update this thread when I have a resolution.