One thing you should consider is a small USB stick that just has an EFI boot partition, with the efi boot and the boot.cfg, and is configured to load the kernel from the second hard drive. That way you could put the netbsd disk in the 2nd bay and need the USB to boot, but then not need it once booted. awkward but it could be better than not being able to run netbsd on the machine. That's all on the theory that the EFI bios on your machine is buggy and fails to work with the 2nd hard drive, and is ok on 1st hard drive and on USB>
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