As RRLedford is always saying (and must be getting fed up doing so

) it's not a good idea plugging any HDD into the HPT if you can avoid doing so. It's been known to be very unreliable, even destroying disk drives, although some people have used it successfully.
If you can afford it, I strongly advise buying a Promise PCI HDD controller and plugging your new HDD into that.
Besides, the HPT controller isn't very fast anyway. Probably better off using the regular IDE ports and preserving your data integrity/hardware.