Just to toss my 2 cents in. I have the same issue with some LUNs on my ESXi 4 and ESXi 5 hosts.
I have a feeling that its on the SAN side also, but we don't control that and their answer is "they are all set up the same way". When they make changes to existing ones, I see that, just "some" new LUNs don't show up til I reboot the host.
Right clicking on the HBA and picking rescan, picking Rescan All (from the storage adapters), etc does nothing for those few that don't show up.
Across multiple versions and patch levels of hosts also.
FC HBAs using Hitachi back end.