ok, I know what you are talking about and I have also witnessed VirusTotal detecting malware from AV engines when it is not detect by the installed AV.
Several times I have noticed this with Avast, after doing some checking the Avast engine on VT was just flagging false positives. The only thing that comes to my mind is maybe VT is not using current signatures that removed the false positive detections.
Another thing that I noticed is when you scan a url with VT if any part of that url has malicious links the complete url is listed as infected.
With most AV's you can go to the same url and it will not be detected unless you click one of the malicious links.
VT is not 100% reliable, it is a good start for references but I would depend more on my installed AV and my own knowledge by checking digital certificates of the file and verifying it is safe.
On VT results, always click on File detail and look for "Signature verification". if the file has " Signed file, verified signature" then it is safe no matter what the AV engines detect.
I'm not sure if VT has the option like most AV's which will ignore Signed files and will not detect them, maybe that it is reason for false positives detections.
I have seen files on VT detected as malicious because of adware like OpenCandy which to me is ridicules. Adware installers that have opt-out options should not be detected as malicious. These adware installers are digitally signed by many trusted sources and will not do anything malicious. Maybe install some junk trialware, toolbars, or change homepage and default search, but they always have opt-outs if the user pays attention. These adware are important to keep programs free.
Thanks.