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My computer takes literally hours to boot, in order to get it all the way through boot, it takes hours to finish saying "Windows is starting" (I'm not sure how long, I went to bed), then when I get to the login screen and type in my password, it takes another 2+ hours to get to the desktop.

My first thought was that this was caused by hard drive failure, as I had been running a defrag and there had been a power failure in the middle of it, so I booted into an Ubuntu Live session and checked the SMART data, which didn't report any problems. Not entirely trusting that data I booted into UBCD and ran a disk diagnostic from there, it reported 1 bad sector and fixed it. The computer still wouldn't boot. At this point I was pretty sure I had ruled out physical failure.

I then ran Testdisk, which also returned no errors, except for this:

"MFT corrupted MFT mirror corrupted repair failed".

But unless I am mistaken about the nature of the MFT,that cannot possibly be the problem. Because it is my understanding that the if the MFT is corrupted, then the file system becomes unusable. But I can access the file system just fine, both from a Live Session and Windows Explorer.

I then ran Spinrite, as it is known for fixing problems no other tool even claimed existed, but it didn't seem to do anything. But when I booted into the Windows install disc and ran chkdsk (which when run previously, returned no errors) it found and fixed an error, having found 1 file and reallocated it.

Optimistic, I rebooted, it still won't boot in any reasonable amount of time. Does anybody know what else I can do?

It won't boot into safe mode, no matter how long I leave it; I left it overnight and in the morning it was still stuck loading "classpnp.sys". "System Repair" hangs at "repairing your computer" and if you try to cancel it says "this operation cannot be canceled", I have left this on overnight as well, to no effect. SFC/SCANNOW run from the install disc returns "there is another repair operation in progress, please reboot and try again" but rebooting returns the same error.

A few notes:
+It's a laptop
+There are no USB devices connected
+I already backed up the drive
+I have run multiple disk diagnostics, scanning each disk sector one by one to find errors, none were found, it is not physical failure.
+If I clone the drive and replace it, logical failure will be cloned as well

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    Reformat and restore from backup. – Ƭᴇcʜιᴇ007 Sep 18 '13 at 17:53
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    This really sounds like a HDD problem. Have you thought of creating an image of the HDD and just restoring the image on a new HDD? Just because S.M.A.R.T passes does not mean there isn't a physical problem with the drive. – Ramhound Sep 18 '13 at 17:59
  • Did you try unplugging all USB devices except for your keyboard and mouse before starting? – Rik Sep 18 '13 at 18:04
  • If you can get to Windows after 2 hours, it seems like a software problem (driver, bad updates and so on). I had the same issue many times on different PCs, and yes checkdisk found bad sectors, another software showed me MFT errors, I stuck on classpnp.sys. In my case restoring registry from RegBack helped me every single time, and I got OS back without reinstalling, no errors occured. – Jet May 17 '14 at 13:33
  • @jet It was a bad hard drive, I did all of that, there hadn't been an update in weeks, and the drive had super slow read times even with linux live sessions – Devon Muraoka May 19 '14 at 18:41
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I would heed the bad MFT warning. Although I can't say 100% over the internet what's wrong with your machine, you did some nice troubleshooting. The fact that it's slow before Windows even loads (safe mode, startup) indicates the problem probably exists in hardware, not the OS. I say this because System Repair doesn't load your user OS, but a diag version of Windows, the chances of the problem existing in both spaces is slim (even if it were a corrupted driver, it would have to be corrupted in both the client OS and system repair, unlikely).

Corrupted MFT is also a red flag. It's probably why everything takes so long, it's trying to read one or both MFTs before determining they're dead, or actually does recover info from them (the 1 file chkdsk found, for example).

Also, I don't think SMART data will tell you about corrupt data on the disk (which TestDisk did), only physical failures, of which it only found one. I'm not sure how the other tools work, but I can give you another test: Get a different hard drive and install Windows on it. If you get the same problem, you have completely ruled out your hard drive, but I have a feeling it's the culprit.

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    @MDMorre313 if it is logical failure (i.e. corrupted data) wouldn't replacing the physical drive and wiping the partition table do the same thing? – Devon Muraoka Sep 18 '13 at 18:17
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    @ChuckFulminata remember, the MFT is not the MBR, which is (most likely) the partition table, unless you're running a GPT. Windows probably tries to repair the MFT before moving on, and Windows has a lot of files. Also, I didn't mean start copying data onto a new drive, just a clean rebuild to eliminate or narrow down to the hard drive altogether, logical or physical. Of course, back up your personal data as soon as you can, but other good answers and comments have hinted to that, and I thought you sounded proficient enough to know that so I left it out :-) – MDMoore313 Sep 18 '13 at 18:36
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    @MDMorre313 Oh, I see, you're saying that the problem is most likely hardware, and that by replacing the hard drive I have eliminated that variable. If the problem persists, it is some other piece of hardware. – Devon Muraoka Sep 18 '13 at 18:41
  • Also, I know that you meant a clean install and that the MFT and MBR are not the same (Testdisk says the MBR is fine by the way) – Devon Muraoka Sep 18 '13 at 18:41
  • @ChuckFulminata you got it, simple, but effective. – MDMoore313 Sep 18 '13 at 18:42
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As @techie007 suggested, you should start anew.

  1. Boot from a live CD and backup any important data you have to a reliable storage device.

  2. Boot from the installation CD/DVD, erase the partition table and make a new one with the partitions you find suitable for your needs.

  3. Install your new system

  4. Configure the system to your liking and make sure the hard drive is now OK

  5. Place your important data back on the hard drive

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