Windows 7 boot error autochk program not found skipping ... BSOD

Hi People,
I been having a on going issue with a partition /boot error

I created 2 PC's from Storage craft shadow protect backup images .
Using the storage craft 3.3 boot cd i created the 100mb  partition and allocated the rest to the system image. restored the windows 7 HP 64bit image.

I then used startup repair to fix the boot settings to boot correctly.
Windows 7 runs perfectly as long as it is switched on .
I have a 1 TB USB harddisk and windows 7  backup running  daily.

After random periods of time after shutdown and power off I get, (partitcularly after a few days off) :
autochk program not found skipping /autocheck

i have tried chkdsk , bootrec repairs to no avail

when i look in the registry remotley with PE it seems the 2 partitions are swapped ie the 100mb is c and d is the windows partition ???? setting the partitions back did not seem to fix the issue , neither did any of the recovery options in the PE disk..

So i do a windows backup restore , and the machine works for a week or 3 and then this happens again ...

I have replaced pretty much every part thinking its hardware :
Motherboard, RAM  HArddisk , the problem still re occurs !!!!

Its got to be due to the USB HDD or some partition scrambling going on but i dont know how to isolate this ...
Im wondering if i should remove the 100mb partition all together , as i do not use bit locker

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if you can remove the HDD from the external case, then you can run a diag on it easily
you can use UBCD for diags :      
noxchoGlobal Support CoordinatorCommented:
Your auto check gets blocked in registry somehow. First of all when it works you need to find out if the Windows starts when you disconnect USB drive at all from this machine.
Kramer8uAuthor Commented:
I use falcon 4 boot cd way better, there is nothing wrong with the drive as stated before, this is the second new drive installed and second motherboard , it HAS to be software the whole machine has been replaced 1 part at a time..

At this point I have no USB HDD connected, my auto check gets blocked in the registry?
I am waitning for the symptom to reoccur . But I can only assume that the startup files get damaged either by the USB being connected or somehow the registy.
 I did try , system restore but it does not fix. So i assume whatever happens actually modifies/damages startup.  
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noxchoGlobal Support CoordinatorCommented:
When this problem happens look on the system C: drive if you have there autochk.exe file. Best if you boot the BSODing machine from some boot CD and look from it.
noxchoGlobal Support CoordinatorCommented:
Also check in HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager right pane in BootExecute if you have any path for check.
Kramer8uAuthor Commented:
thanks for the tip , im waiting for the problem to happen again will get back to you soon
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Kramer8uAuthor Commented:
OK I forgot about this !!!

I had found a Solution myself !!!!!!!!

What the problem was Is shaodow protect sets the small 100meg partition as "Active" or i had restored usiing th boot disk slightly wrong.
 Upon repairing the boot records with the windows 7 disk the system works fine until a random period of time.

That random period of time I found out is when a windows update is installed that requires files that are in use to be updated. Usually a security update.

After the update is applied , the registry some how gets mixed up upon next boot and the small 100 meg boot partition is considered the active boot/system partition and it thows this error because the files do not exist !

To solve this I had to boot using a boot CD and:

1. You can either remove the 100meg partition if you do not use the encryption feature of windows 7 with a partition tool.
In my case i had to do this as the auto repair tool in windows 7 kept "repairing" the 100 meg partition as the boot partition which i did not want.  So I deleted the partition and left it unformatted .

2. The most important step !! you must set the other partition IE c: d: ( the rest of your windows drive" as "active" with a partition tool, you should see that the 100meg partition was "active" you must move the "active" partition to the C: drive. ( if you do not do this the auto repair feature of windows  7 wont work !!!).

3. Reboot from the windows 7 disk  make sure you select the correct  version 32or 64bit and select repair you computer , You have to do this 2 times.

3.1 the first time it will not find any windows 7 installs , the auto repair will  scan for them and ask to reboot.
3.2 the second time you will see 1 windows 7 setup in the list , again the auto repair should this time add the relevant boot files to the "active" partition (step 2).  you can use bcedit if you are having issues. Then ask to reboot

Viola a fixed booting windows 7 that next time does a windows update will not repeat the autochk error ..



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Kramer8uAuthor Commented:
I had found a solution and it is posted above.

I did not find any reference anywhere online to my solution and there fore request it be added to the solutions. I think this is possibly the only solution to this issue that acually works and took me 2 weeks to figure out.
Kramer8uAuthor Commented:
I found my own solution via trial and error.
The experts comments unfortunatley did not help me isolate the error or lead me in the direction that solved my issue so I did not award any points.

Buit thankyou for your contributions guys , it was a tough one !!! 2 weeks it took me : (
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