This replacement is much more powerful than the factory amp. and I wonder if that sound you're describing is the amp shutting off and powering on again because of the voltage is dropping below a certain threshold.
I had this Sony amp in a 3-speaker setup (2 regular speakers and a subwoofer, all within specification). The bass hit the same as my old factory amp but weirdly after 1-2 songs, it would just go silent. If I turn on/off the headunit, the Sony amp happily sings. One day later, It happened again and so I pulled over. The Sony amp, was a normal hotness and the indicator light was a steady white light (not a flashing red). I cycled my headunit again, and played some non-bassy music and the amp never went silent. I did notice when I first had the Sony amp installed, the indicator light would slightly dim when a bass note hit on the subwoofer.