The 3 foot is below the roof line you said? If that is the case, you're more than likely getting reflections from the roof since it's a top loaded coil. The antenna is going to look for a ground plane of some kind. This is not an electrical ground but more or less what it uses to keep the signal "Up". If it's at ground plane level, it can have adverse affects on the antennas resonant frequency. Have you tried adjusting it at the tip? You might be able to get it better in the higher channels, but as you shorten it, you'll sacrifice some on the lowers.
More than likely, a 3 footer isn't going to work in your application and/or mounting location.