Many motherboards today come with the option in BIOS to boot from an external USB drive, such as an external hard drive. However, if the boot priority is set so a USB drive is booting before your internal root hard drive (or sometimes, even if the option to boot from USB is just enabled) then it will not let the computer boot properly. The best thing to do is go into your BIOS and see what boot devices are enabled. If there are any options for a USB device, disable it. It can cause more problems than anything. We just built a new RIP station that actually will not boot properly even if the Flexi dongle is left in the USB drive if the option in BIOS is not disable to boot from a USB device.
BIOS menus vary from system to system so it is hard to give you a step-by-step instruction for disabling a boot option without knowing your system. However, the general idea is like this: Boot into the BIOS when your computer is first loading up. Watch for what button you need to press to enter BIOS, it is often the Del button or F12 button or similar. When you enter the BIOS, you will be searching for a section usually called Boot Devices or Boot Order. This lists the type of drives that your computer will attempt to boot from, along with the order in which it will try and boot from them. When you look at this list, there will generally be a few different boot devices. Your primary hard drive (where your Windows is installed) should be listed, along with a floppy drive (if one is present in your computer) and CD/DVD-ROM drives. There may also be options for booting from an external USB device, or on the rare case through a network interface card (NIC). Somewhere on this screen should also be a description of what you need to press or do to enable/disable a boot device or change its priority. If the option is to enable/disable, then you want to find the Boot From USB option and disable that one. If the option is just to change around the boot priority (which devices the computer will try to boot from first) then you want to move the Boot From USB option to the very last priority.
It is very important when you are working in BIOS, especially if you are new to it, to be very careful. I suggest taking your time, and before you even go changing ANY settings, just open in to BIOS and search around and if need be google some of the options and menus you are seeing, but just be careful changing around any settings and be sure the changes you make are ones that you want.
I would say just try to remove that option from BIOS first, and see if your computer will boot up properly. Then, check to see if the drive is being recognized. If for some reason it is all of a sudden not being seen in your My Computer list of drives, check in the Disk Management tools. This can be located by going to My Computer -> Control Panel -> Administrative Tools -> Computer Management and select the Disk Management section. In this window should be a list of all disk media on your computer right now. That means your main hard drive, any additional hard drives you may have in your computer, USB thumb drives, even CDs or DVDs in the ROM drive. Check to see if a drive is shown there that matches to your external hard drive. Does it say the drive is active, formatted, etc? Often the easiest sign that it is alright is that when you click on this drive, at the bottom of the screen the "status" bar of the drive is blue and not black. If it is black, that generally means the drive is inactive, not formatted yet, formatted in a way that is unreadable by Windows, or that there is a problem with the drive.
