Noise can come from different things. Power,EMI and or ground loops. The first test I would do is take a ground wire from the radio and attach on your amp. If that didn't work putting a cap in the system is reducing the voltage spikes in your car and filters the voltage so that could be a case and I've seen in the past if you have an older and or inexpensive amp, noise could be radiated from the power supply. I'm not knocking your equipment but you didn't tell us what you where running. Even if it's good equipment, things can go weird.
You might even have a bad cell in your main battery.

It's not easy removing noise and sometimes you just have to try different things to get the noise to stop.

I have 3400 watts of power in my system and every time I get a noise I know my voltage between my two batteries are freaking out. That's the price I pay for the system.

3400 watts=(if real watts) 283 amps of draw at full tilt at 12 volts.
Not magic it's ohm's law like mother nature: can't be fooled.