While I am not sure, is here a possibility that your program might conflict with Sofraid. I am using a 20113 Mac Pro, which I bought this year 'cause I did not know they were coming out with . . . oh, never mind. Anyway, I had to get a box, put 4 2TB disks in, using thunderwhateever, and presently, things are not working well, but are working. The few times I have done the csrutil thing, it seems that things deteriorate after each reboot. I have not rebooted for a couple of days, and things seem fine. Have you had any concerns by others in this area?
Rob