Helping people with computers... one answer at a time.
Your computer's BIOS can be configured to boot from any of several devices. If one looks bootable to the BIOS but isn't, you can run into problems.
Why does my desktop stop booting up with an external 1TB USB drive attached and switched on? It boots normally from the normal internal 80GB drive with the external 1TB drive switched off!!
This happens surprisingly often - I've heard many people mention it.
Typically, they'll just leave the external drive powered off until the machine has finished booting; at which point, they turn it on and Windows recognizes it.
Depending on how you use your machine, that might be the most appropriate solution.
On the other hand, it's also possible that it's a very simple fix.
The problem is simply that your computer's BIOS is looking to boot from an available, bootable USB-connected device before it looks to the hard disk from which it normally boots.
The solution is to change the boot order in your computer's BIOS so that it looks at the hard disk before USB devices or doesn't look at USB devices at all.
Unfortunately, I can't tell you exactly how to do this - the BIOS controls your computer before Windows starts and is unique to your machine (though often common across product lines or even manufacturers).
You'll need to check your system documentation to determine the exact steps. In general, when your computer boots, there's a key that you need to press right away that causes the BIOS to enter its configuration mode instead of booting Windows. Then, somewhere in there should be an item called "boot order" or something similar. In that, you'll want to make sure that your hard disk is checked before the USB devices if you want to boot normally while that external drive is connected and plugged in.
Your computer's BIOS is programmed to look for a device from which to boot. It typically works something like this:
Is there a floppy disk inserted? Try to boot from that. (Even if your computer has no floppy disk, it's very likely that your BIOS still includes this option.)
Does the hard disk have a recognizable boot sector? Try to boot from that.
Is there a CD or DVD inserted and does it have a recognizable boot sector? Try to boot from that.
Is there a USB device inserted and does it have a recognizable boot sector? Try to boot from that.
If none of the above apply, give some kind of "no bootable device found" error.
The boot order in the example above is: floppy, hard disk, CD, USB. As mentioned above, you can typically alter the order in which the BIOS checks for devices from which to boot.
Things get a little interesting because of this phrase, "Does it have a recognizable boot sector?" As I understand it, there's really no standard way to answer that question. In your case, not only is the USB drive earlier in the sequence than your hard drive, but if the BIOS is checking for a boot sector on that device, it seems to think that it's found one, even though there's nothing on that USB drive to boot from.
Here's where things get sticky.
If you actually do have other USB devices from which you occasionally want to boot your machine, you probably do want to have the BIOS check USB devices first.
And not just before your hard disk, but before that other USB device, your external hard drive.
I don't know of a way to control the order that BIOS checks the USB devices if there's more then one.
So you're left with the workaround that you're using now:
Let the BIOS check for bootable USB devices before it checks the hard drive.
Turn off your external hard disk when you boot (be sure to click Safely Remove Hardware if you're rebooting and Windows is still running), and turn it on again after Windows is running.
It's messy, but it works.
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