Hi,
we got this issue on a newly-bought Supermicro board today. After reading the proxinstall script and verifying assumptions on the installed system, I figured that it was caused by GRUB being installed both in EFI and i386-pc modes. This happened due to the machine being set into dual boot mode, which enabled both UEFI and legacy BIOS mode parallely. It seemed that the proxinstall script sets the boot mode variable to efi if the efi directory in sysfs exists, but also installs i386-pc grub unconditionally. Dual boot mode will then prefer legacy boot, which loads GRUB with the unchanged config from before the last update-grub in the installation script.
This sure can be circumvented in the script, but strictly speaking, using that dual boot mode isn't a good idea anyway.
In any case, the installed system is completely functional, and the boot process can be fixed by manually installing and/or removing the irrelevant versions of GRUB.
Cheers,
Nik