From the FAQ:
VirusTotal's antivirus engines are commandline versions, so depending
on the product, they will not behave exactly the same as the desktop
versions: for instance, desktop solutions may use techniques based on
behavioural analysis and count with personal firewalls that may
decrease entry points and mitigate propagation, etc.
In VirusTotal desktop-oriented solutions coexist with
perimeter-oriented solutions; heuristics in this latter group may be
more aggressive and paranoid, since the impact of false positives is
less visible in the perimeter. It is simply not fair to compare both
groups.
Some of the solutions included in VirusTotal are parametrized (in
coherence with the developer company's desire) with a different
heuristic/agressiveness level than the official end-user default
configuration.
(Emphasis mine)