We have an iSCSI SAN unit connected to a cluster of ESX servers. The servers are all managed by an instance of vCenter. The vCenter instance manages a dozen Windows Server VMs.
Most of the VMs have more than one volume. Those volumes appear in the VM settings in vCenter. Drive C in Windows appears as Hard disk 1 in vCenter. Drive D appears as Hard disk 2, and so on. In other words, the SAN is obfuscated from the servers.
One server, however, is configured differently. Its C drive is handled by vCenter, but its second volume is directly connected to the SAN via Windows iSCSI Initiator. When I asked the server admin why he had configured it that way, he asked, "Why would you want a middleman handling your volumes?" I tried to explain that vCenter's HA and Snapshot features won't cover the second volume, but he remains unconvinced.
I remain unconvinced as well. Though it seems like all the VM's volumes should be handled by vCenter, I could be wrong. Have you configured your VMs in a similar manner? Something where the boot disk is presented to the VM by vCenter, but all other volumes are directly connected to the SAN?