When Imaging machines with UEFI enabled i am running into a problem after rebooting from WinPE. the first reboot does not see the hard drive. If you check BIOS before it attempts to boot there is not option for the hard drive or windows boot manager under the UEFI options. After it fails to boot, BIOS then registers the harddrive and the machine will boot into windows and complete the OSD template.
... not sure why youre BIOS is not detecting the HDD, but that's a BIOS problem more than anything.
If the BIOS can't see it, then it doesn't matter whether the disk / partition is set to boot active or not -- won't happen, since BIOS can't see it.
You may want to try enabling some HDD-controller compatibility mode(s) potentially, to help you along (details vary based on vendor / hardware) // and / or poke your hardware OEM about any known issues / BIOS updates perhaps?
That's a few levels below what we can / do affect ourselves, normally .