In answer to all the responses...
I have added the FC cards WWNs to the Filer. I have zoned the HBAs ports on the Brocade and saved then enabled the new zoning config. The host was presented with the LUN and added to the map group. I have done this many times before with other servers and HBA configurations and never seen this issue, ever. The only thing I have different on this server is that the Hypervisor-OS is stored on an SDcard and there is no local hard disk... Nothing elses is different. I have blown it away and reinstalled twice now and I am thinking the next step is to just put the ESXi 5.x Hypervisor oin the machine and see if the cards can be seen via that. I have also tried swapping the QLogic cards out for a spare pair and redone all the configuratrion stuff I spoke of earlier. Thanks anyways folks.