What media player are you using? If your using the limewire player it isn't very good and tends to skip. Try using a different one and see if you get better results. Have a look at this thread:
CODECs list and alternate players for Movies
If thats not it they could be corrupt files. Sometimes it's a matter of trial and error until you find a good file. So don't give up
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As far as the crackleing goes, I don't see how that could hurt your speakers. Unless they crackle all the time which could mean that one of your speakers is bad.