SOURCE: Alpine CDA-7840
Some 4-Runners have a factory system that uses a separate amplifier to power the rear speakers. In this case you need to activate the amplifier using the blue/white remote output from your Alpine deck. It sounds like the wire that activates the amplifier is currently attached to the deck's blue "power antenna" output, so that the amplifier is only on when the tuner is selected. Disconnect whatever is attached to the blue wire behind the deck, and attach it to the blue/white wire instead. That should solve the problem.
HU harness color code pretty much universal.
red=ignition
yellow=battery +
black=ground
blue/white=remote turn on
blue=power antenna
pink/black=audio interupt in (not sure if you have one)
speaker wires
gray=right front
violet=right rear
green=left rear
white=right rear
speaker wire with black stripes is negative.
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