I had the same problem with a Pioneer Mono amp in my Girl's car. At first thought it was the amp, but plugged it into my car.
Next, I replaced all of the remote wiring, and it still did it. (It is probably a remote problem btw, I'll explain now)
Finally, someone threw a random post about checking the fuse box. I ignored it at first, but then my girlfriend said that her car charger and mirrors were not working properly. She stated that the mirror motors were extremely weak, and that her car charger light would go on, but the phone wouldn't charge.
I checked the fuse box, and low and behold, the fuse was blown, but the melted metal was close enough for some power to arc across the gap. This was enough for the amps to play for 3 seconds, and then the car's electrical would shut off the line, then restart it when it gained enough voltage.
If you have your remote wired into anything other than your deck, check that lines particular fuse.