For everyone's clarity, Tommy is using a Rode (not Red) NT1 A mic. It's a studio grade quality and is not the cause of his problem.
Tommy, in the Vocal harmony window, under the Harmony section (middle window), make sure the green On button is displayed. Below it, there is a gear icon, which opens the Detail Setting window. There are three pages of settings. Try adjusting the settings on Page 2. There is likely a setting that is preventing either mic from doing what you want.