Proper partition alignment is important for good disk performance. It is not
usually an issue when partitions are created on a clean disk. However, there
are circumstances under which it can be an issue. E.G., if a partition is
converted from FAT to NTFS, and depending on the parameters chosen, a
partition is created which crosses a boundary. The result is that a file
might be allocated storage on space that is divided by the boundary. The
result is an increase in the overhead for each read or write operation.
Also, proper choices are important when creating data structures on
solid-state disks.
This is probably not the place for a an extended, deep discussion of
underlying concepts and methods. So let me refer you to something to give
you a taste of one dimension of the topic
http://www.ocztechnologyforum.com/forum/showthread.php?t=48309
Tom Ferguson