Vista 0xc000003a error on boot during scan after SP1 and virus removal

Vista on a Dell Inspiron 1521 laptop. This laptop was infected with a couple of trojans and rogues as well as other malware. I used Malwarebytes and it found and removed 40 some variations. It was also installing SP1 at same time. Once SP1 was done I rebooted. It begins to boot but right after the Windows screen with the moving bar it goes back to a white text on black screen and begins a scan that appears to be Malwarebytes or some other "scan on boot". I am presuming MWB since that is what i had scanned with.

It lists 98xxx files and begins scanning. When it gets to 580 / 98750 it halts and reads:
! 0xc000003a ! (MPEngine.dll)

It sits there until I turn it off and restart. It won't start in any safe mode, it just gets past loading all of the drivers and stops. I can boot from Vista DVD but it tries to repair and fails and reports that it cannot repair.

I am thinking if I can shut off the boot-on-scan then I may be able to boot up and get things repaired to where it will boot consistently again. I need to apply more Vista updates and SP2.

Thanks in advance for any help.
 
You will probably have to re-install Vista fresh... Malwarebytes isn't a virus removal tool, but it is an indicator that your computer is badly infected
 
I believe there is a much better and quicker solution than just re-installing fresh. MWB is much more than an indicator of problems, it is a very effective eradicator of some very difficult variations of malware. It certainly found and fixed the rogues and trojans. The OS isn't broken if I could prevent whatever process is running the scan on boot. It could be chkdsk, it could be Spybot, it could be MWB but no matter which there has to be a way to stop it from running at startup. Something either in the registry or in a startup config file is telling it to scan before booting into Windows. I can appreciate your perspective but that is really the info I would like some help with at this point.
 
Please mark this as "solved". I was able to get past the error and successfully boot back into my Vista (with SP1 successfully installed) system...no fresh install required! The problem was related to the reboot in the middle of the SP1 install as suspected.

Thanks for your encouragement and support.
 
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