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Although you might be able to send the file to Avert so they can check it, since the program is "home grown" and a one-of-a-kind thing, I doubt they will fix the virus definitions to skip your program only. Still, it might be worth a try at the link below.
I can see their side of things.. You have a customer asking: "How can I make my virus not show up as a virus in your scanner?" Since the scanner is probably detecting something within the program which is used in other malware, I don't think you'll get their approval to remove that detection. Every virus writer in the world would like to have that information...
In your situation, we simply set up the program as an Exclusion in McAfee.
Hope this helps.