Dave--they have an automated system that crawls the web, joins the site if possible, sees how many e-mails the site sends out, checks a few downloads, sees if the site attacks and alters your browser, etc.
Check the "Detailed Analysis" to see the files it considers harmful:
RED
startbarfader3-11.exe
HUD.Vision_by_Jiri_Mahel-v2.2.exe download analysis--
HUD.Vision_by_Jiri_Mahel-v2.0.exe
YELLOW
Dark_Rainmeter.zip
Vista_Ultimate.zip
I noticed that "Generic Trojan" is indicated, which makes me think that it's a false positive; for instance, Norton 2010 antivirus calls the Silica DesktopX widgets dangerous even though they are not. Sometimes it is behaviour of a file, not because it contains a known problem.
In any case, there is a section where the webmaster can make a comment.
Nobody from McAfee comments; that section is for users to make comments. They have a system where if the commenter is "correct" or not, they get rated, and their comments can be "trusted" or not. I'd recommend that the webmaster comments, and some of your users. You can get them to retest it, explain the likelihood of false positives (if that's the case), and get a green rating.
Even WinCustomize had a red rating until someone did something about it.
