LED Clock Dimming, Normal?

I have a completely stock system.  The car is a 97 Grand AM.  I use a tape adapter to run my D-LINK MP3 player though it and every time the bass hits hard my LED clock dims considerably.  The only thing I can think of here is the fact that the MP3 player also has bass boost that it's causing the stock speakers to draw more than they're supposed to.  I don't know a whole lot about car audio.   It doesn't do this when just using the stock tape player.

The battery is not quite 3 years old, but I tested and it's reading 12.69 w/o the car running.  The alternator was also replaced less than 2 years ago, and I've had this problem both before and even days after it was replaced.   Is this normal?  The headlights don't dim, but the LED clock does.

Just curious as to if I'm hurting anything by doing this.  I've noticed that most people don't have this problem w/ stock systems.