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PC refuses to boot to desktop with external USB3 HDD's plugged in at startup

Level 7
I recently upgraded for the first time since August 2009 from:
AMD Phenom X2 550 BE, RoG Crosshair III Formula Mobo, 4gb DDR3, Geforce 250GTS, 320gb Seagate Barracuda HDD (60+260 partitions)
Intel i5 6600, RoG Maximus VIII Hero Mobo, 16gb DDR4, Geforce 760gtx, Samsung 850 250gb sata SSD (OS), 3tb internal WD HDD.

I had an internal 1tb HDD start dying on me and before it gave up the fight I moved all my games and media to an emergency external WD Elements 3tb USB3
drive. Both the old and new PC's ran/are running Windows Ultimate SP1 64 (When I finally managed to install and boot into it but that's another story.
TLDR: USB bootdisk wasn't working so went the DVD route followed by a BIOS update to get to desktop)

My current issue is this:
The old PC booted up fine with the 3tb WD external connected at startup along with another WD 1tb external. When I try to boot the new PC with the external
drives connected however, it either boots straight to BIOS , where I choose the windows bootable Samsung 250, only to either be returned to BIOS again or to repair windows
or startup windows normally. Choosing either of these two options either loops me back to the the same screen or back to BIOS. If I then switch computer off,
unplug the drives and start up, it gets to the login screen with absolutely no problem.

I have checked the boot devices and only the Windows bootable 250 is selected. All other options are disabled.

Is there a BIOS option that could affect this that I am not aware of or what might be going on?

Thank you very much for any possible help.
Shout if any additional info is required.

Jones0610 wrote:
The REAL fix would be to get a clean, formatted external HDD and copy over the files that you want to save from the current external HDD. I suspect, as ricemanhk said, that when you copied the files onto the external HDD it already had a bootloader or fragments of a bootblock on it. If it were me, in the interest of speed and effecting a permanent fix, this is the approach I'd take.

Just to add to that, remember to delete ALL partitions on the external HDD, even the main one. Then create a new partition spanning the whole volume and give it a quick format. That's the only way to ensure no hidden partitions exist.

Also when you look in disk management, right click the partitions and select properties. There you can see the partition style MBR or GPT.

In your BIOS boot tab, is CSM disabled? That could also force the board into UEFI mode only.

Sorry to jack this very old thread but I've just spent hours trying to rectify the exact same problem and surprisingly there wasn't very much detailed info on how to fix this issue, aside from people saying to unplug the external HDD prior to boot and then plugging it back in, which is tedious and not very ideal.

I just bought the 10GB Seagate External Backup Plus Hub (with the 7200rpm Barracuda Pro inside :)) and my PC refuses to boot with this connected via USB and I've tried basically everything mentioned earlier and could not get it to POST/boot. I'm running a Strix Z390-E with a Samsung 970 Pro 512GB NVMe as my boot/system drive for reference.

The ONLY workaround I've found that completely eliminates the problem in the meantime is to go into the Boot Configuration section inside your UEFI bios settings and find the option for something along the lines of GPT/MBR recovery policy and set that to Auto Recovery. It will then (hopefully) boot again normally every single time again like mine now does.

Hope this helps.