Hopefully you did not operate the amp with no speaker connected to any particular channel. You must always have a "load" (speaker connected or the amp may blow. Most modern amps have sensing protection to cover you, but don't take chances.
To test the amp, always keep things simple:
>with the power off
>disconnect all speakers from the amp that have the problem - only keep the known good-sounding ones connected
>use your mp3 player as amp input music signal
>get some known good speakers out of the house or wherever...these will be connected to the suspect channels
>fire up the amp at low volume level, increase vol gradually and listen for problems
If the same bad noise is still there, your amp has blown something.