I believe it's a firmware issue. The reason Windows server not booting up is that it's scanning for boot image using HBA. Unload HBA drivers from the BIOS of the windows server. It should work then. ( Unless you are booting from SAN ).
Also, check the driver compatibility of the server HBA with the Data ONTAP version you have. You may need to upgrade the firmware. Consult NetApp Global Support Center for this piece of info.