I've got a Windows 2003 virtual server. The VMDK files are sitting in a NFS datastore on NetApp storage. The windows 2003 server was originally physical and I P2V'd it in to vSphere. I then block aligned the VMDK files using MBRAlign.
I am now upgrading from Windows 2003 to Windows 2008, will this affect the block-alignment as I understand that Windows 2008 doesn't need block aligning?
New partitions created using Windows 2008 are correctly aligned. However, if you do an UPGRADE (assuming this is possible) and your partition was not previously aligned, it will not become magically aligned. I have had little success with running mbralign with a Windows 2008 partition, so make sure the partition is aligned before you do the upgrade.
Also, you may have limited success with P2V. I seem to recall an instance in the past where we ran P2V on a Windows 2008 server and it resulted in misaligned VMDK's which we didn't seem to be able to fix.