When connected via FireWire, FireWire800, or USB, there must be a drive in the first bay (top bay of Fusion D400Q; left bay of Fusion R400Q); otherwise, the hard drives in the other drive bays will not be recognized. If hard drive is connected via SATA, there is no issue.
Another manufacturer's previously-installed SATA driver may be accessing a Sonnet SATA card in error causing a drive access slowdown. For example, we have seen Fusion D400QR5 performance drop from 200MB/s to under 50MB/s in such circumstances. The solution is to remove the other manufacturer's SATA driver.