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System Partition Restored - But How Do We Restore the MBR (Windows 8.1)?

Following yet another windows collapse which even Rollback couldn't resolve, I've managed to restore a cloned system drive I backed up a few weeks back, using Partition Wizard. But my attempt to also restore the mbr I backed up the same way at the same time (to its own partition) has failed. The result is a working system but every time I reboot, I get the "system needs repair" screen.

Using bootrec.exe /rebuildbcd I bullied the mbr into recognising that there were a couple of OSs to launch (the clone and the restored partition) and now it presents the "repair" screen but I can use the F9 option to select the restored partition and away it goes. Everything hunky.

My question is: how do I lose the repair screen which is clearly looking in the wrong place or has a flag set which doesn't get removed even after a successful boot?

It may seem like a trivial inconvenience and, if I'm sat in front of the machine when it's rebooting, it is trivial. It adds perhaps 20 seconds to the reboot process. But this is my main home security workstation, which runs my surveillance cameras when I'm not at home and also has my main repository of support tools or software which I occasionally need to access when I'm away from home. And systems occasionally shut down for a variety of reasons - eg powercuts. I need to know that, when the power is restored, my machine will reboot, without human intervention, at least to the stage I can login remotely and enter the final boot password through logmein.

And stopping at the repair screen prevents that...

Two associated supplementary questions:
1 How should I have copied or restored the mbr in order to avoid this issue?

2 One of the really irritating discoveries I made during this episode was that not only were my system disks for Windoze 8 rejected by the automatic repair system but that even on my working windows 8.1 systems, if you try to create a recovery disk, they all tell me "We can't create a recovery drive on this PC - Some required files are missing. To Troubleshoot problems when your PC can't start, use your Windows Installation disc or media" - which, of course, is hopelessly stupid advice if, like thousands of us, you've performed your upgrade to 8.1 without such a disc or media. So how do we create such a recovery disk for 8.1?
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Gregory Miller
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FDISK /MBR repairs the MBR in OS through Win7. Do not have an 8 to test on currently.
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Actually the commands you've applied do not edit MBR. They are for editing BCD.
Recreating MBR is done through FDISK.
And even if you do this the message you get will not go.
Have you let it try to repair once the system? For Windows 8/8.1 it comes always when new hardware or system disk clone operation has been detected by Windows itself. Thus you need the repair to run once. Otherwise it will not remove this dirty bit.
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Apologies: I obviously didn't include enough info.

@technodweeb, nobus

I had already "repaired/recreated" the mbr (using bootrec not fdisk) in order to get as far as I have. But that itself was a defeat and is precisely what I'm trying to avoid for the future. What I need to know is how to back up an MBR in perfect working order so that it, in a similar situation in future (which, in my experience, is inevitable) I can restore both the mbr partition and system partition and be up and running with minimum hassle.

Perhaps I should explain why I need to restore precisely the same mbr rather than receate one and that is because I use Rollback, which stores its hooks in the MBR (which also causes problems, particularly when some of the windoze updates also modify the MBR - see the lengthy discussion which took place over that issue here:   Rollback still haven't resolved that issue, though I have noticed that, so far, in 8.1, none of the updates have caused that MBR problem)

I take your point about editing the bcd not the mbr and stand corrected. However, my point was that it was only by doing that that I could persuade the system to accept that valid OSs were present and available to boot from. It clearly isn't "remembering" that choice. So I'm looking for a way to force it to.

re "need the repair to run once" - that's what I figured but see Supplementary question 2. The point is I CANNOT run the repair because I've upgraded to 8.1 and windoze now rejects my 8.0 installation disc as an invalid media.
you said you restored a cloned system - that should include ALL data, also  the MBR
perhaps that was lazy use of the term "cloned". What I actually did was create a low level binary copy of the system partition AND the mbr partition using Partition Wizard (which, as far as I'm concerned are clones). Then, when the system collapsed, I used the same software to copy the partitions back again.

What software would you recommend that would achieve what you're suggesting would have happened had I "cloned" it the way you understand cloning to work? My understanding, up to now, is that none of the cloning software will simultaneously clone 2 partitions (the system and the mbr). They'll either do a single partition or a single drive. And the single drive is not a viable option as my system partition is the smallest partition (other than the mbr) on a 1.5 Tb drive and I have no intention of cloning the whole drive.

If you're suggesting that there is a cloning option that will somehow cope with two partitions as an integrated entity (instead of two separate clones), that may be the answer to my main problem, which is how to get back to square one (an installed system ready to run with all my important application software) without having to bugger about with mbrs and windoze repairs.

It doesn't, of course, deal with the issue of how to "repair" windows 8.1 given its rejection of 8.0 installation media. But I'd happily live with that if I could find a working answer to the main problem.
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Disk 0 is the Drive which includes the system partition. There are 7 partitions on that drive. I have three other internal drives and one external (which contains the system clones)

I have to be careful using chkdsk because it can damage the Rollback snapshots. If I have cause to suspect disk damage, I tend to uninstall the Rollback, run Spinrite overnight, then reinstall. But I should stress that disk/file damage is definitely not the issue here. I began the initial installation and cloning only after a thorough Spinrite session in the first place.

Are you (both) saying that if I'd created the clones with Paragon, I wouldn't have this problem? i.e. it would have correctly restored the MBR as well as the system partition?

If so I'll give it a try for next time.

Meanwhile, any ideas on how to get around the spurious Repair prompt? Or how to create a standard recovery disc for Windows 8.1
Have you tried recommended steps here:

And yes, with Paragon it should not cause you such problems.
>>  Are you (both) saying that if I'd created the clones with Paragon, I wouldn't have this problem? i.e. it would have correctly restored the MBR as well as the system partition?   <<  yes - thats what i say
Right, I'll get the free Paragon then.

As to that interesting link to the procedure for getting a legit 8.1 iso, that's a good find but what a palava!!

That is a ludicrous bunch of hoops to jump through just to get an installation disc. That's not your fault, of course but I find it impossible to believe that Microsoft hasn't made it somewhat easier to get the software we need to conduct what they must know are going to be routine repairs!!

I have a number of issues with that route, not least that I no longer possess a machine running Windows 7 (which is required to perform the download). All 3 of my personal machines are now on 8.1, one of which is 64 bit and the other 2 are 32 bit. So I'd need two different Windows 7 machines (1 per processor type). I do have access to a couple of my own customers' 64 bit Win 7 workstations but it would be awkward to tie one up for a couple of hours downloading the software and, off the top of my head, I can't even think of someone with a 32 bit Win 7 machine I could hijack for the task.

It's also not clear how it would react to entering a Windows 8 licence which had already been used for the 8.1 upgrade.

Let's go back to square one. If I remove Rollback, and recreate the MBR, is that going to defeat this "Your System Needs a Repair" problem?
I think no. But you can try it.
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Found the actual solution myself but splitting point to the 2 experts who suggested Paragon to prevent re-occurrence