I have a LUN on Windows 2008 Server and if l got to Disk Management on the server l'm picking up two disks from a Single LUN. The FC connection from the server to the Switch is on a single port HBA. I have MPIO software installed on Windows 2008 Server? Is ok to see the LUN as two drives?
(I believe your post is in the wrong place though)
It's definitely a bad thing - the host should see just one LUN. But what puzzles me is this: are you 100% sure you have just one path from the host to the filer?
IF you have more than one path then MPIO is not good enough in FC environment - you need DSM to properly maintain multi-pathing. Have a look at this:
Given a NetApp clustered system, you will see 2 paths to each LUN and you will need multipathing (MPIO) software. For iSCSI, Microsoft's MPIO is sufficient but if FC you will want NetApp's DSM.