Bootmgr.exe missing after BIOS Flash Update

Archiver · Oct 2, 2016

Hi guys. A month or so ago I upgraded my PC, including a new ASUS Z170-A Mobo, and an i7 6700k CPU. I was running smoothly off the BIOS version that had come on the disc for about a week, but then I was instructed by ASUS tech support to update my BIOS version whilst trying to troubleshoot an audio issue I was having.

Long story short... I have 2 internal drives. 1 being my 500gb SSD with windows 10 + other stuff on it... 2 being my 1tb HDD with games / media and whatnot on it.

Before I updated my BIOS, windows would boot no issue with the proper hard drive (my SSD) being in boot priority slot 1 in my UEFI BIOS settings menu. However, ever since I updated it will tell me "BOOTMGR.EXE is missing, press ctrl+alt+del to restart"

For whatever odd reason however, if I move my HDD (non-OS drive) to the 1st priority in the boot sequence, my PC will boot no issue. I have no idea what caused this to happen... but it has been annoying me for weeks on end.

Solutions I've tried so far include resetting my BIOS settings to default, repairing my PC with the Windows installation disc, and a couple other things - but nothing has worked. My only worry is that if my 2nd drive were to ever fail on me (it's about 6 yrs old at this point), or I were to replace it... I wouldn't be able to boot my damn PC!!! I would love to get this minor annoyance fixed now before it becomes a massive headache down the road. Thanks in advance for all the replies, and I'll be checking on this post at least once daily at the minimum

[OS = Windows 10]

SuperSoph_WD · Oct 4, 2016

Hello there, @Archiver!

Did you have both the SSD & the HDD connected to the system when you were installing Windows 10 onto the SSD? If you did, you are most probably encountering an OS Confusion which is why you are experiencing these errors.

I'd recommend you post a screenshot from Disk management in Windows, so I can see for sure if that's the case.
You could try repairing your system from the Windows Installation media with the HDD unplugged! This could help fixing the bootmgr on the SSD.
Otherwise, I'd suggest you start from scratch, but first make sure you backup all important data from the SSD & the HDD somewhere off-site! This is a must when tampering with your storage configuration and it would avoid any potential data loss. Afterwards, attempt to clean install Windows 10 onto the SSD with the 1 TB hard drive disconnected from the motherboard! You should also take a look at this Windows Install & Optimization guide for SSDs & HDDs. It would definitely shed some light on how to properly configure your storage without facing these issues again.

Keep me posted if you have more questions!

SuperSoph_WD

Archiver · Oct 4, 2016

SuperSoph_WD :

Wow, thanks fro all the helpful info! Here's a screenshot of the disc manager as requested. I'm about to try and repair the OS with just the SSD plugged in via my installation media. Will post back with results! http://imgur.com/a/c1NSf

Archiver · Oct 5, 2016

Okay, so the repair media did not help once again, and my PC will not boot either with only the SSD plugged in... still needs HDD in + in front of SSD in boot priority queue. =/

Any other remedies to possibly try before starting fresh?

SuperSoph_WD · Oct 5, 2016

This seems unfortunate, @Archiver!
Well, I think it would be best to perform a clean install of Windows onto the SSD with the HDD unplugged from the system. Make sure you have the SSD configured in AHCI in the BIOS settings before beginning the fresh install, though. Once you have Windows up and running on the SSD, plug back the 1 TB HDD and even re-format it through Disk Management (AFTER YOU HAVE BACKED UP THE DATA ELSEWHERE). According to the screenshot, it seems like you have your system partition stored on the HDD and not on the SSD which is why you are unable to boot properly without it.
IMHO, a fresh install should do the job!

Let me know how it goes!
SuperSoph_WD

Archiver · Oct 5, 2016

SuperSoph_WD :

Okay, just finished the fresh install... seems to boot fine now. Here's a screenshot of the new disc manager - http://imgur.com/a/G4YfA

I have another couple questions though. I formatted both drives 100% before reinstalling, but there was on thing that I was confused on - being the "OEM Reserved" portion of my SSD. I formatted it at first, but then ended up Deleting it after some googling. I read that it really didn't matter which option I chose, so I did both. However, after plugging my HDD back in, which used to just be a System E: drive.... now I am seeing a system E & F. System E being 96mb, and system F being my 1TB HDD...here's a screenshot - http://imgur.com/a/bo0z8

I think I am going to hold off installing anything onto this drive until I get a reply from you... but what the hell caused this and why is there that little random 96mb E drive? Should I try deleting / formatting that drive again?

Thanks again for all the help! : )

Archiver · Oct 5, 2016

Alright, tinkering around with the disc manager I think I fixed it. First I deleted the small partition, then expanded the other... but it looked strange, so I then deleted both and created a new simple volume. Now it seems to all be 1 partition, with 930gb or w/e free. Here's some screenshots.

http://imgur.com/a/VCDsE

http://imgur.com/a/VhS7Z

Looking good now, yeah? I see what you mean looking back that my System file was put onto my Disc 1 HDD last time around... what a shame ='[ Now I know from now on to now have multiple hard drives installed while installing OS's. Thanks once again for your time, the help is greatly appreciated

Archiver · Oct 5, 2016

Okay, last post / screenshot... I noticed after looking back at these that 450mb unallocated space leftover from my previous "OEM Reserved" partition (I assume... recall it being around the same size). I extended the main partition to absorb said 450mb. How am I looking now?

http://imgur.com/a/GhHF2

(Note that Disc 2 is my external HDD, in the process of transferring backups back onto PC)

USAFRet · Oct 5, 2016

All that messing around with partitions was not needed.
The BIOS upgrade reset your boot sequence in the BIOS back to the default.
You should have just changed that back to what it was.

Does the system work now and boot up properly?
Does it boot up with only the SSD connected?

Archiver · Oct 5, 2016

USAFRet :

It didn't reset my boot priority though, after the update it still had my SSD as #1 and my HDD as #2, but refused to boot. It wasn't until I flipped them with each other until it would boot. After the fresh install / fixing the partitions it now boots fine with the SSD in #1 priority, and with only the SSD plugged in.

SuperSoph_WD · Oct 6, 2016

Hey there again, @Archiver!

You look good now, indeed! However, @USAFret made a good point about not tampering with the partitions so much. Everything looks great, so there's no need to change anything for now, as long as you are satisfied with your system's performance and there are no more booting issues.

Switching the places of the SSD & HDD might have helped after the reset because it would make sense the default settings to look for the first bootable option the first SATA port available. I'd advise you keep regular backups of your data in multiple locations and always remember that clean installing Windows needs only one SATA device connected to the motherboard. This will avoid such OS confusions in the future.

Best of luck! Hope we were helpful!

SuperSoph_WD

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