If I am reading this right you installed grub to your external drive and that is set to the first boot drive in BIOS. It got skipped over before because no OS and then the Windows drive booted before. Disconnect the external drive reboot...Windows? If yes check your BIOS boot order. If I am guessing correctly the SATA controller driver isnt in Ubuntu. You can poke around to see if the can be found to attempt the install to the internal drive.
Matthias
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