Sorry, I should have reread the entire post. You had already stated that you had only the hard drive selected in the BIOS. Once again, WHICH hard drive is being selected by your BIOS? There is a way of changing which drive is at the head of the stack of drives. I might be stating the obvious to you but it is important...
What is your mobo (be specific, ASUS P8P67 Evo for instance). I would like to look at the manual for it as I think me and Mas are probably right about the external drive being examined for a boot partition before defaulting to your hard drive.

you do have specific motherboard in my specs:
Gigabyte G41MT-D3V

Mirac,
Heh, new to the site so did not realize about the small grey Specs dropdown..
In the manual, there is a hard disk boot priority list (the top line item in your CMOS BIOS settings-Advanced BIOS settings). What does that say on your computer?

1. Primary,
2. External,
3. Bootable add-in cards

Thanks Mirac, see if you can DISABLE items on 2 and 3, the external drive and bootable add-in cards. That might prevent Windows from checking them out on boot up. It should not affect Windows being able to see them ( I hope...).

I don't know how. There are no options nor anything in the description or the manual...

I can only select which goes first, wich second, which third. And internal is the first...

Heh. In order to CHOOSE which drive is 1st, 2nd, or third, you HAVE TO HAVE a dropdown box when you highlight your choices and hit ENTER. For instance, highlight your 2nd hard drive (use the arrow keys of the tab key) and hit enter. Your list of attached hard drives should come up, including your external USB drive. There usually is a DISABLE choice in there as well. Choose DISABLE for your 2nd and 3rd hard drives to prevent the BIOS from selecting the USB drive.
Also check to see if your INTERNAL drive is actually your Hard Drive inside the computer and not the USB drive...
If that does not fix it, I am done with ideas. Good Luck!

I have only one hdd in the dropbox. I have option of choosing which hdd first but not in there. I can't disable certain, or do not know how.