Hello,
1. For virtual machines:
I had this issue on VMWare environment. I did use the mbrscan and the mbralign to align the boot partition. You can find them on the Netapp Host Utilities Tool.
Check the link for it:
http://blogs.netapp.com/storage_nuts_n_bolts/host_utilities/
2. For physical machines:
I see one option for physical machines, dont know if its going to help you but here it goes.
2.1 First lets start with a non-boot partition alignment:
You can use diskpart to align the partition.
check the link:
http://support.microsoft.com/kb/929491
*if its an old partition you need to map a new LUN to the server, create a new one aligned and move data.
You can use the diskpart to check if the partition is aligned.
2.2 Now for one boot partition:
1 - Map a new LUN/Share on your filer to you physical server.
2 - Create one aligned partition using diskpart. http://support.microsoft.com/kb/929491
3 - Use any backup solution for backing up your old partition and restore to the new one. could even be the ntbackup
4 - Change boot.ini.
5 - Reboot your server.
6 - Change you HBA boot config, point to the new LUN.
7 - Unmap your old LUN at your filer.
Check this link:
http://www.tuxyturvy.com/blog/index.php?/archives/59-Aligning-Windows-Partitions-Without-Losing-Data.html
Note: Windows 2008 creates the boot partition aligned.
Or you can use some partition tool, ^^.
Hope this information can be useful.
Thanks.