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There is a chapter in my book "Storage Area Networks for Dummies" that includes a step-by-step process for configuring SAN boot drives, and some of the "gotchas" that can cause what you are experiencing.
Things to look out for:
1) Be sure to use the latest version of boot BIOS on your adapters, and follow the instructions included in the readme file that comes with the driver version for setting up the boot BIOS correctly.
2) When using more than one HBA in the server, set up both HBA's for boot, and make sure your path-failover software supports it. Doing so will allow you to survive an HBA failure.
3) Make sure the system BIOS is not trying to boot from any internal disks. You can verify this by disabling the internal SCSI adapters in the server, and re-trying the boot.
4) Make sure the HBA topology setting is correct for your environment (FCAL or fabric)
5) Make sure you use "single initiator zoning" in your fabric to the port where your boot drive is located. In other words, simply zone the HBA you are booting from to the storage port where the boot LUN is ported (do this for each HBA in the server). In my experience, If you have more than one target port in the zone for the boot HBA, the BIOS may get confused during boot, and you will experience the exact same symptom you are getting.
6) Get the latest tech-tips from Microsoft on SAN booting technet.microsoft.com and search for SAN BOOT.
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