It's been a while since I last work on the Perc, but when I had more than one array, the speed was much slower for each array.
i.e. I had a mirror for the o/s and 5 x 2Tb raid 5 array on the one controller, all running Sata drives. When I moved one array to a second controller, the speed was much faster.
Also check your arrant isn't performing some consistency check as that will slow it down.