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I have installed Win8 and Ubuntu side by side before in the past and had issues with booting which were fixed perfectly the first time using boot-repair. This time, I installed Win8.1 and Ubuntu with the same issue. Boot-repair also fixed it. After running Windows a few times, I attempted to reboot and got the following:

Error:  Unknown Filesystem
grub rescue>

I was able to find the windows UEFI boot file doing a boot options from the BIOS and successfully boot Win8 from: MS/Boot/bootmgrfw.efi. When I booted into Unbuntu Live from a USB and reinstalled and re-ran boot-repair, it was much more involved and asked me to open a couple of terminal windows and paste in some additional commands. At the end running, it said everything was good but I still have the same issues. It appears it made backup copies of my UEFI boot files because now I need to boot bkpbootmgrfw.efi to successfully load Win8.1 while bootmgrfw.efi gives the same unknown filesystem error.

The URL I got after running boot-repair the second time is Is there a way to manually fix the UEFI boot or should I blow away UBUNTU, repair Windows and then reinstall UBUNTU ?

Update: I can boot \efi\ubuntu\grub64.efi and get to the normal grub boot menu which I can load either Win8 or Ubuntu. It also shows the boot file for Win8 to be the backup file.

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Glad you found a solution. If you boot /EFI/ubuntu/shimx64.efi do you get the GRUB menu too? – LovinBuntu Dec 4 '13 at 21:54
Please post your solution as an answer. – RolandiXor Jan 11 '14 at 23:58
Please post your solution as an answer please. – Joe Feb 17 at 22:22

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