500.1 amp power lights blinks on and off

Try checking the earth it may not be earthing properly if there is paint scrape it off as it wont earth properly with paint there or try a different earth point. The remote wire switches the amp on and off try shorting that and putting 12v through it to keep it on constant just to see if the cd player is not keeping the amp off.

Protection mode; follow this link to get a manual for the amplifier: http://mobile.jlaudio.com/products_amps.php?amp_id=439

Below information is from the manual:

Status Indicator Lights / Protection Circuitry
There are three status indicator lights on the top of the amplifier. These are as follows:1) "Power" (Green): lights to indicate that the amplifier is turned on and operating normally.
2) "Thermal" (Red): lights to indicate that the amplifier has exceeded its safe operating temperature, putting the amplifier into a self-protection mode, which reduces the power output of the amplifier. The red light will shut off and the amplifier will return to normal, full-power operating mode if the heat sink temperature drops back to a safe level.
3) "Low ω" (Amber): lights to indicate that the impedance of the speaker load connected to the amplifier is lower than the optimum impedance load range for the amplifier. When this light is on, a protection circuit engages and reduces the power output of the amplifier. The amber indicator will also light when a short-circuit is detected in the speaker wiring (this can be a short between the positive and negative speaker wires or between either speaker wire and the vehicle chassis).
There is only one condition that will shut down an undamaged 500/1v2 completely… If battery voltage drops below 10 volts, the entire amplifier will shut itself off. The green "Power" indicator on the top of the amplifier will turn off when this occurs. The amplifier will turn back on when voltage climbs back above 10 volts. This may happen in a rapid cycle when bass-heavy program material causes a weak charging system to dip below 10 volts momentarily. If this is happening in your system, have your charging system inspected to make sure it is working properly.
For information on troubleshooting this amplifier, refer to Appendix E (page 21).