I purchased a code signing certificate and all looks well. When tested inside a clean Virtual PC OS I no longer get the "The Publisher could not be verified" message.
So just for grins, using a hex editor, I change a few constants in the VB6 exe which I see on a form. And the VB 6 exe still runs wihout any error message.
I thought the code signing certificate would tell you if the file had been changed in any way?