when Norton does it's nightly scan it states that it has 2 Master Boot Record? Occassionaly it will say also that it has only 1. Is that normal?
No that is not normal. And if you are running Symmantec Norton Antivirus 2004 or 2005 you are in great danger of virus becayse of the servere limitations in scan options, both mentionend cannot scan some system files, system restore files etc. wich serverly compromises your safety, also they make some specific flaws that makes some virus run on your machine ONLY because you have either of those two version, i don't know if it is fixed in the new 2006 version though. Some of the best out there is the free Avast Antivirus, Trend Micro also do carry some very good programs, same goed for F-Secure wich is also prefered by nearly every school here in Denmark.
