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I have a Seagate FA GoFlex Desk - 2000 external hard disk. I use it with a Dell Dimension C521 desk top. The internal HDD of 160 GB is dedicated to running Windows Vista Home Premium (32 bit) OS. The PC BIOS can boot off the USB. The GoFlex drive has Seagates pre installed instant back up program etc. I used shrink volume to reduce the single partition to half the size in order to install Linux distributions in remaining space. Till this point the drive was recognised as bootable by the BIOS.

I wished to first install openSUSE 12.2 with Grub 2 as bootmanager. The plan was to set up BIOS booting sequence to internal DVD, external HDD and last the internal HDD. This way if the external drive is not connected or switched on the system boots into Windows and if the external disk is connected the boot manager comes into play. This had worked with earlier version installs with Legacy Grub.

I opted to install Grub 2 to the /boot partition which is a primary partition (the second on the external drive). The install appeared to have gone OK and this partition shows up with bootable flag in GParted. "BUT" the external drive is no longer bootable! BIOS does not recognise its presense nor does Windows Vista bootrec program when I tried to repair possibly damaged MBR. The first primary partition containing the Seagate proprietary software is available to windows OS. Gparted can see all the partitions. Only I cant boot off the drive!

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Not sure if this will solve all your problems but have you considered using Plop boot manager. It lets you boot from any device even without BIOS support.

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