Sounds like you might have a ground loop between the devices on the audio channel, how close to the power wiring does the audio wiring from the GPS to the AMP run?
I got this effect really bad when my laptop was plugged into it's charger and mains speakers, the closer the power wiring is to the speaker wiring, the less feedback there is.
Quick check for it, plug an mp3 player into your amp at the gps end (assuming its a standard 3.5mm plug), if its ground loop, the ungrounded mp3 player won't have the whine.
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