what amp is it? not all 400 watt amps are created equal. take your sub for instance. It is realistically an 800 watt sub snce that is its RMS power. the 1600 watt rating means that it withstood 1600 watts for a burp on a test bench. no guarantee how long it could sustain that amount of power. Also, power ratings for subs mean net to nothing in most cases. you can make a "300 watt" sub powered by a 200 watt amp tickle your ears and rattle your trunk. to find your problem I would need more info. How is the sub wired? dual 6 ohm coils is an odd impedance and will lead you to either overload your amp or not get as much power as you should from it. what size is the box? an undersized box will severely limit your output.
as for the sub box differences, a ported design usually has a bit more boom versus the tighter sound of a sealed box. I prefer sealed myself and I have gotten massive bass from sealed designs.