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Help answer this question below.
I'm assuming that you are speaking of Windows
In safe mode the system has only critical functions 'on'
in normal start up the virus scan may miss, or handle the infections differently.
the easiest part of Windows to attack is the registry
http://www.snapfiles.com/reviews/ERUNT/erunt.html
this backs up windows registry
,viruses hide in system restore, so sometimes you have to turn off system restore and then scan.
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