File system alignments are important in a virtual environment. If a partition within a virtual machine is not aligned correctly, additional load can be placed on the storage array. Windows 2008 R2 by default should use the correct alignment parameters, but older Windows versions may not. To check the alignment, launch a command prompt with administrative credentials and use:
wmic partition get BlockSize, StartingOffset, Name, Index
Divide the StartingOffset by the BlockSize. In the example below, the value would be 63. This would be an example of a misaligned partition. The offset value of 32,256 is a common value for a misaligned file system.
The value for the next example would be 2048 for the first partition. This partition has correct alignment.
More information concerning this command can be found at http://support.microsoft.com/kb/929491.