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.
You are using a SATA port that is not port-multiplier aware. For example, the internal SATA ports in a Mac Pro that may be brought to the PCIe rear panel via an eSATA extender cable are not port-multiplier aware. All of Sonnet's Tempo SATA cards with external ports are port-multiplier aware.
