My only guesses are your head unit is eating up too much power for the battery, or the battery needs a recharge to handle the new load.
Additionally, my guess is a control switch in the head unit is defective. I had a 700W 4-channel amp hooked up in my Celica last year until I accidentally pulled out the power cable, which in turn shorted out the control switch. With the control switch fried it ate up my car battery and killed it essentially. Replaced the amp and jumpstarted the battery, and the car still runs fine to date.
I would recommend bringing it to a shop in your area though that does audio installs for cars to see if they can remedy the problem if what I mentioned isn't the case.