I think I know what is going on. I can explain it using my second v6 Lite system-2 with the smaller drives which has been working fine for long time and still working now. It has 2x18 GB and 4x146GB drives, OS is booted from 2GB USB drive, the drives configured as two H/W RAID (Dell Perc4) units 18GB RAID-1 and 546GB RAID-5.
As you can see on picture 4 there are four volumes: 100GB and 200GB iSCSI, 120GB and 118GB FC.
But if you go back to the unit picture #3 there are S001 18GB and S002 546GB hardware RAID units, but in addition there are also both FC volumes presented back to the system itself as units S003 and S004, despite FC card is in target mode. It means the physical drives are calculated in the total storage limit twice - first as the actual RAID units and then as the FC volumes!!!! It is definitely a bug, and I think it appeared after the server was connected to a FC switch, before I was using direct HBA-to-HBA connection.
And I know it is the same issue with the server I posted originally about, the only difference for that system-2 the total storage size is still within 2TB limit even if counted twice (2 x 546GB=1.092TB), but for the bigger system-1 it wrongly exceeds the limit. I can't post any units/volumes snapshots because the management interface just reports "Total storage size exceeded licensed storage capacity". But if I go to the console and run hardware info I can see the same problem: two actual h/w RAID units S001 and S002 plus two FC volumes from the same server, and take a look at the volume serial numers - FC volumes listed twice (S003/S005 and S004/S006) for each of two separate FC cards. So the disk are counted three times: as the RAID units and then twice again as the FC volumes!!!
How can I exclude FC volumes from that double count? Probably if I create a non-default FC group and allow only client initiators it would work, but I don't have access to the GUI anymore. Is there any other way to configure FC groups? Is there any way to apply temporary eval license to access management?