so, here's my setup:

Infinity 10inch 1000-Watt(RMS) Subwoofer
400W Xplod AMP
and using my 2000SI head unit (theft reasons )

Well, after 20 minutes of listening to music, my bass fades in and out, just the bass. I was wondering what is wrong. Is my amp too weak? my head unit?

thanks in advance.

Sounds like your amp is being worked too hard, next time it fades, pull over and feel tha amp, my suspision leads me to believe that it will be extremely hot.