I am facing the same issue since past weeks, I have not able to figure out the what is causing the problem but I did find the solution.
Boot into the installation media, Go to shell
efibootmgr -v
if the qubesOS entry is missing add it manually
efibootmgr -v -c -u -L QubesOS -l /EFI/qubes/grubx64.efi -d /dev/sdd2 -p 1 #grubx64.efi for qubes R4.1, xen.efi for Qubes R4.0 Sdd is the drive and p 1 is the partition no
Reboot, You will find the boot entry for qubes.
Edit : I think the it’s the motherboard firmware causing this particular issue, Please update your motherboard bios firmware to latest and disable C state option.