Hi Andre,
In some cases when I was upgrading the ESX to ESXi hosts, it took ages to boot up for more than 4-5 hours. I'm not sure what happened to that host, but Googling around points me to the number of LUN that is presented to each and every hosts in the Cluster from my EMC FC SAN array, at least in an average the ESX 4.1 host before the upgraded got around 15 VMFS 3.3 datastore presented and approximately about 12 VMs with more than 12 RDM Physical mode present to it as I host multiple MSCS cluster as well.
I guess that is the issue that I'm facing during the upgrade from ESX 4.1 to ESXi 5.1, and then after long hours of the booting process, some of the newly upgraded ESXi 5.1 cannot see the LUNs as it was previously in the ESX 4.1, no hardware changes of config changes on the EMC FC SAN array and not NFS datastore. This is halting me to convince the management to do the major production ESXi 5.1 upgrade affecting 450 VMs and 55 VMhosts.