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Repair Failed

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Boggin:
Windows Update doesn't work in Safe Mode which is probably why SURT wouldn't run.

You need to run that findstr cmd to produce a cut down version of the CBS log which shows what sfc /scannow could and couldn't repair, but at least you've got rid of the MSE errors.

Having two antivirus programs installed can cause anomalous problems and certainly slow a machine down.

I'm not sure if McAfee could have corrupted MSE but I think it would be a good idea to also uninstall McAfee which you can do by downloading and running the MCPR.exe

http://www.majorgeeks.com/files/details/mcafee_consumer_product_removal_tool.html

You can do this in Safe Mode with Networking but run it twice, rebooting after each.

You may notice an improvement in normal mode after running it the first time.

When you boot into Safe Mode, all 3rd party programs including AV programs are isolated which is why your machine works okay in that mode.

If you are using the Premium version of Malwarebytes Antimalware (MBAM) then I believe a particular update did cause problems, so a uninstall/reinstall of that may also help but if you are just using the free version of MBAM, go Start - type services.msc and press enter.

Scroll down to and right click on the MBAM service and select Properties then use the dropdown to change its status from Automatic to Manual.

Click on Stop - Apply - OK then click on File/Exit to close the services window.

I use the free version of MBAM and this is how I have mine set.

If after doing all of that and your machine works better in normal mode, then try SURT again to resolve the corrupt manifest error.

For the time being while you don't have an AV program installed, Windows Firewall will afford you some protection, but I think it would be best to try and repair your system without any interference from security programs.

KatieWar:
Thanks again for all your help. I actually just did a custom installation of Windows 7 from the disk. I’ve located my old files and I am moving them into the new version. It seems to be working!

Boggin:
Well that's one way of doing it :)  and as long as you remember to only ever use one antivirus program then you should be okay.

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