Windows 2003 Black Screen Blinking Cursor at Boot

I recently had a software mirrored (RAID 1) hard disk fail on a server. On reboot I assumed everything would be ok as windows writes the correct path in the boot.ini to the second hard disk. Unfortuantely when i rebooted, all i was left with was a black screen at the point where Windows 2003 would normally kick in, with a flashing cursor and no error messages.

I checked the boot.ini via the recovery console, also ran fixboot but no luck. Anyway, after reading up on fixmbr, and ignoring the warning it gives, the server booted up off the second drive fine.