Following further testing I have some more information on the problem.
Using a an ESATA to SATA adapter cable I attempted to connect the HDD docks directly to the mobo SATA ports(both blue and grey). The drives remained undetected. but POST and boot became very slow. Clearly the controller sensed a connection else the POST behaviour would not have changed, still communication was not established.
With the same adapter cable I then connected a variety of HDDs as well a an optical drive to the ESATA ports. The drives weren't detected.
Encouraged by the implications of a slow POST I borrowed an OCZ Throttle ESATA flash drive. The Throttle worked perfectly connected directly to the ESATA port or to the adapter cable plugged into either set of SATA ports.
Edit:
I am convinced this is a firmware issue as the hardware has been exonerated.