So just wanted to confirm this..With VM running Windows 2003 with multiple Drives, the VM is kept running for the MBRAlign tool to collect the drive information. And it shuts its down when the information is collected.
Then it goes and fixes the offset (while creating a backup copy which can be deleted later) and ask the user to power on the VM on the ESX console from where we are running MBR tool.
Instead of using the older mbralign tool which was available with the ESX Host Utility Kits, you can now leverage the new version of VSC to perform an "online alignment" of a VM, without having to power it off. This would determine which partition within the VM is generating the largest number of partial writes, then it will allow you to create a datastore which is offset by the inverse amount of the VM writes, effectively negating the misaligned writes by shimming them.
You can read more about it in the Installation and Administration Guide for VSC 4.1, under the section "Optimizing and migrating datastores and virtual machines". This section has a segment called "Types of Alignments" and explains the differences between functional alignment and actual alignment.