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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.

Hi ogkspaz

Welcome to the ROG forum.

It's likely just the external drive giving you problems with the new platform, you could leave the external drive disconnected until you're booted into windows then connect it.

That is how I'm currently doing it as a workaround yes. It's mostly from laziness that I don't want to have to do this each time.
What worries me most is that the old PC had no issue with this whereas the new one just refuses to cooperate.

It might be best to transfer everything off your external drive onto an internal drive.

I've had similar problems in the past but not on M8 hw specifically.

Any chance the external HDD plugged into the USB port is bootable? It could be that the BIOS is trying to boot from it for whatever reason and obviously can't. You didn't say how you created this backup. If it is a clone it could well be causing conflicts and confusion in the BIOS. Personally, I wouldn't bet my life that just because USB is not in the boot priority list, the BIOS still won't try to boot from it (due to a coding bug or whatever).

The obvious thought would be to go into the boot settings and disable USB boot from the list. Boot priority one should be the device that contains the OS that you actually want to boot from. Until you get this sorted out, I'd disable any other boot device choices. I know you said you checked this but if it boots ok with the external drive disconencted but doesn't boot with it plugged in, that sort of narroes the field of possibilities.

Running the latest BIOS version? Of course the latest BIOS version could have introduced this problem as a new bug 😞

There's a setting in the boot section of the BIOS designed for speeding up the boot process. Even though it shouldn't effect your issue (if no USB is in the boot priority list) it's worth checking.

In the USB enabled setting, there's a choice along the lines of partial support..... basically, set it so that the BIOS doesn't even look at anything connected to USB ports during bootup.

Sorry but I'm doing this from memory so I can't recall the exact setting choice names.

The backing up was a simple case of "copy and paste everything that I want to keep". This was mostly pictures, videos and games. Steam, Origin, etc. BIOS is the newest one at 2202. I'll check out the USB setting when I get home from work this evening.
Another thing that might be worth noting. Save and exit after you change boot sequence in bios says: You have not changed anything. Save and exit anyway? (Paraphrased)

Possible causes:
- There's a hidden boot partition (for some reason) on your external HDD, the BIOS sees this and is trying to boot from the external HDD
- Maybe it's a conflict between MBR formatted external HDD and GPT formatted SSD? BIOS sees external HDD and goes into legacy mode while your SSD runs UEFI?

My previous laptop came with an HDD, I added my own msata SSD and reinstalled windows on that, but because the HDD came with the hidden boot partitions, it was never created on the SSD for some reason. Ultimately I had to take out the HDD first and then install windows with only the msata plugged in, and then manually delete the hidden partitions on the HDD as it would otherwise throw an error on boot.

Post work update:
Checked Hard drives in disk management. Both just say NTFS - Healthy (Primary Partition)
Only the C Drive has 100MB EFI System and the 232GB (Boot, Page file, Crash dump, Primary partition)

The only relevant USB setting I can find in BIOS was:
Legacy USB Support [Enabled]
[Disabled] The USB devices can be used only for the BIOS setup program. It cannot be recognized in boot devices list.
[Enabled] Enables the support for USB devices on legacy operating systems (OS).
Disabled sounds good but all it did was make my mouse not work in BIOS. Still refused to go into Windows.

I'm not sure if this matters but something I haven't mentioned yet is that when it starts up it gets to the screen where the 4 Windows colours come together only to be replaced a split second later by a black screen and the white bar at the bottom that says "Windows is loading files..." as if I was busy with a fresh install.

I agree with ridemanhk. If the machine boots fine with the external HDD disconnected and doesn't boot correctly with it connected, there is something on the external HDD that is competing in the boot process.

The "easier" fix would be to totally disable booting from the USB. This is explained in a youtube video in the sticky threads section of this forum. It's in a video that explains how to streamline the mobo for rapid booting. My mobo is not a hero so I don't know the exact setting. Apparently, the BIOS will poll USB ports for a bootable device even if USB is not in the boot priority device list. This is obviously different than the way most BIOs work.

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.