There's a lead on the tuner that's intended to control the antenna. It should go up and down with the activation of the tuner. I think that this is very neat, but it sounds like it's not how you have it hooked up. I'd change it if I were you. I hated to have my antenna up for no reason when I was playing mp3s. Also there's a slight bug in some of the antenna controlling hardware out there. You could fix it if you have the problem.
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Bitt Faulk