06 Saturn Vue

My GF 06 saturn vue is giving me issues. I am far from a mechanic, but have done some worked and used these videos. Back to the matter at hand. We recently replaced her alternator. Since then, when we start it, the lights on the dash blink on and then shut off as well as the stereo. We have shut it off and restart several times until the lights stay on. It does affect the electic locks and windows. It only happens when the vehicle hasnt been started in over 8 hours. Every dealership wants attleast a hundy to look at it. What are your thoughts.