ok, here's a posting I found on the web. according to this, maybe your remote is connected to the ignition as opposed to the radio remote lead.

4. I've had a new amplifier installed and every time I turn my car on or off my speakers pop. Is there anything I can do to stop the popping?
The most common cause we see of speakers popping when a new amplifier has been installed, has to do with what is called the 'remote turn-on lead', or 'wakeup lead'. This wakeup lead is what tells the new amplifier to turn on at the proper moment. The wakeup lead should be connected to a wire exiting the factory radio that is typically labeled as 'amplifier turn-on lead'.

For a variety of reasons these two wires sometimes do not get connected to one another. Instead, to turn the new amplifier on, its wakeup lead is connected to an ignition source. Doing so leaves the new amplifier on any time the car's key is turned on. The reason a pop is caused by this method is that the amplifier is 'awake' when the audio signals come from the radio. A small voltage "blip" accompanies the very start of the audio signal when the radio is turned on. Systems are designed for the amplifier to "wakeup" shortly after this blip enters the amplifier - thus the blip is never heard. If the amplifier is already awake when this blip comes through, it amplifies the blip, turning it into a pop.

Some vehicles do not have a turn-on lead that is compatible with aftermarket amplifiers - the vehicle may use a 5-volt signal, but the amplifier needs 12 volts in order to turn on. SoundGate's TRIGLOHD interface remedies this situation, transforming the 5-volt signal into a 12-volt turn on lead. A low-voltage factory amplifier turn-on lead will be found in many Ford Motor Company vehicles, Lexus automobiles, and Infiniti automobiles.




Turn on thump can vary from a slight pop to a mind shattering, teeth rattling BOOM! This thump is caused by the audio circuitry stabilizing when power is applied. Most amplifiers and source units have muting circuitry that lasts a couple of seconds to allow these fluctuations to subside before passing a signal. However, if the amplifier un-mutes before the source unit or any other accessory, you better watch out. Here are some things to try if you have turn on thump.

Verify that the amp has a good audio ground reference. (See rule 6 of the Ten Commandments of noise free installation.)
Don't install the system so the amplifiers can be switched on when the source unit is turned off.
If you still have thump, add a turn on delay module in line with the remote turn on wire to the amp.



Q: How can I stop the annoying "thump" I get when turning on my stereo?

A: This is a common problem. When you first turn on your system, the turn-on signal going to your amplifier causes a pulse that produces a nasty thump or pop in your speakers. The way around this is a thump muting circuit. It uses a relay to eliminate the thump.


http://akamaipix.crutchfield.com//gr.../noise_faq.jpg
That should answer it