Upgrade the firmware of the card and install the web interface.
There may be an "2TB Auto-Carving" option in the configuration of the web interface. I'm not sure if it's present in PATA, but I know it's present in SATA controllers. Also, for such a large array, I would consider using LVM and partitioning.
There is an auto-verify setting and media error scanning setting that may being running ad infinitum. Enable write cache for that controller. You may want to check out all those options in the web interface as well.
Also, for that number of disks, you will gain speed in a RAID 10 configuration. RAID 5 is fine, but 10 typically beats it out for performance on large drive clusters.
Additionally, consider upgrading the card. The 9500S-12 is intended to be used for what you are doing(enterprise). It has 128MB cache and is benched between 4% and 90% faster than your card due to the redesign. It also has a battery backup(ordered separately) for write cacheing to your array- which is nice if you have a power blip.
Lots of things you can do all in all. I have the same setup on my fileserver, but with 120 GB drives. I wish you luck.