The Vsphere client does not allow you to create offset LUNs.
You would have to use a combination of fdisk, and vmkfstools
See
http://kb.vmware.com/kb/1009829
For more info on this
You can look at the following for the netapp best practices document
http://media.netapp.com/documents/tr-3747.pdf
If you created a datastore that was misaligned by the EXACT amount you needed to bring the VMDK into alignment,
the VMFS blocks would be misaligned and this would cause the same IO problems.
See page 9 of the netapp paper for a drawing of this.
I would suggest just going through and correcting the alignment of all of the VMDKs
Regards