well....it sounds to me that you have the wrong remote wire connected to your amp. If your head unit has a remote wire and power antenna wire then most likely you have your remote hooked to the wrong one. I could be wrong but you may want to check your connection again.
I have never seen this situation occur like you have explained it, however this was the most logical situation I could think of. Also more information about the head unit would be nice.
Good luck.
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