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0e1f616
(Get the code!)
I have seen what I believe is the same problem several times with ubuntu-server edition.
* Boot up from USB stick (possibly this forces EFI mode?)
* Install, everything looks fine
* Reboot, machine doesn't boot :-(
* Turns out that the machine has msdos partitions but grub-efi was installed, rather than grub-pc
I see the following as possible issues, but beware that I am certainly no EFI expert.
1. If the disk has MSDOS rather than GPT partition table, I don't think EFI booting is possible. In that case I think grub-pc should be installed instead of grub-efi. In fact, it should probably also check that there is a suitable EFI boot partition too.
(Or: perhaps grub-efi should always be subject to confirmation, always giving you the option to install grub-pc instead)
2. The ubuntu-server text-based partitioning doesn't appear to have any option to create a GPT partition table. At least I have just tried this with ubuntu-12.04 server in a VM, and it doesn't offer me this choice in manual partitioning.
This is rather forces people to continue to use legacy partitioning and booting. If you know what you are doing you can boot from a live CD, partition with gparted, and then reboot into the installer.
3. Actually what I said in (2) is not true if you use "expert mode". At the point "Create empty partition table on this device?", you can select gpt. But expert mode is painful and tedious.
Another solution would be if "Create empty partition table?" in non-expert mode could offer the option of GPT. Or to avoid another prompt, it could automatically create a GPT table if you booted in EFI mode and grub-efi is going to be installed later. Maybe it does this already, I haven't tested it. But this still doesn't help if the disk has a pre-existing msdos partition table and you don't remember to overwrite it.
(Aside: I have just tried installing an ubuntu server VM in virtualbox with EFI enabled, using expert mode and gpt, but it wouldn't boot and dropped me into EFI shell instead. I told you I wasn't an EFI expert :-)