I don't think they are related. When the Check Engine" alarm goes off, it does interrupt the head unit so that you will hear the alarm. This is by design. You could completely disconnect your stereo system to diagnose whether the check alarm stops happening, but my bet is that it will continue and has nothing to do with your stereo. Good luck!
"This one goes to eleven." 2007 ProStar 197 TT w/MCX and Powerslot.