You need to know the block size of your disk, or the stripe size on a raid/LVM. Misaligned partitions happen in cases where the blocks of the filesystem are not 'aligned' with the blocks on the disk (or chunks in a striped environment like storages, RAID or LVM).
So, if you have a 8k chunk size on the storage, use 8k block sizes on the host filesystem.
Also, the first partition on the disk will lose 63 kb because of the MBR, start your partition (using fdisk) on the next chunk/block boundary. Example: you have a 64k chunk on your RAID/Storage array, so start the partition on the 128th kb so you will be aligned to the 2nd chunk in your array.
Good info here: http://www.vmware.com/pdf/esx3_partition_align.pdf
To check the current alignment do a fdisk -l on the disk you are using:
# fdisk -lu /dev/sda
Device Boot Start End Blocks Id System
/dev/sda1 * 63 97659134 48829536 7 HPFS/NTFS
As you can see, it is starting at 63 (right after the MBR) so its probably unaligned to the disk block size. Most people recommend you to use 128 but this value can change depending on the disk cluster size.
Unfortunately, you have to re-partition your drive to fix that, but maybe using some tool like parted you may be able to change it 'on the fly' or at least without the format.