A colleague of mine pointed me towards your blog a while ago and I've been reading it for a while - good work. Normally I don't comment, but this entry echoes an experience I've been having.
I run a F17 and Windows dual system, where F17 and Windows are on separate disks each with its own EFI partition. When I unplug the F17 disk and boot the system, then (on next shutdown) plug the disk back in, the BIOS "can't find" the EFI bootloader on that disk. It is there. I can put it back via the livecd and grub2-install, which crucially prods the BIOS to update its boot order.
Curiously, however, the same sequence applied to the Windows disk brings the Windows Boot Manager back. Which is just as well as I don't have a PE disk capable of running bcdboot or whatever incantation is needed for Windows (yet).
This sounds like a similar issue to what you're seeing. I'm going to dissect my BIOS tomorrow and see if I see strings.
I see something similar
I run a F17 and Windows dual system, where F17 and Windows are on separate disks each with its own EFI partition. When I unplug the F17 disk and boot the system, then (on next shutdown) plug the disk back in, the BIOS "can't find" the EFI bootloader on that disk. It is there. I can put it back via the livecd and grub2-install, which crucially prods the BIOS to update its boot order.
Curiously, however, the same sequence applied to the Windows disk brings the Windows Boot Manager back. Which is just as well as I don't have a PE disk capable of running bcdboot or whatever incantation is needed for Windows (yet).
This sounds like a similar issue to what you're seeing. I'm going to dissect my BIOS tomorrow and see if I see strings.