VMDK Disk not aligned

I am working with both VMware and Netapp on this issue and when I run the scan on my Symantec Messaging Gateway vmdk its showing that it isn't aligned properly on the disks. If I try to run the manual alignment tool provided by Netapp or the P2V tool on the vmdk it basically blows up the vm and the vm doesn't start which I expected. How can we get this vmdk into alignment? I tried this with both version 10 and 9.5 and have the same misaligned disk issue.