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When connecting my android phone to my laptop. I don't think it gets to the point of booting harddisk, so I don't believe this is relevant, but for completeness, it is a dual boot Ubuntu 12.04, and windows 7 with grub.

Primary boot device in BIOS: HDD (even tried bootable flash memory, and it, as expected, booted the HDD)

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In the BIOS, aside from the boot list is there also a "HDD" list? It may be recognized as a USB HDD and being put at the top of that list. – Ƭᴇcʜιᴇ007 Jun 8 '13 at 19:37
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Is this really a problem? Just connect your phone after booting starts. – terdon Jun 8 '13 at 19:38

It is probably trying to boot from the phone. Simply go into your BIOS settings and move "internal hard drive" to the top if the list. It may be slightly reworded, but I'm pretty sure you can figure that out.

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