The battery is charged, all connectors on the battery look clean and dry, when I turn the key I get a clicking sound, headlights start flashing. I went to open the driver side door, low beeping sound and the car started to roll my window down even though I wasn't asking it to. Thoughts?

 

Do you mean a repeating clicking sound or just one click?

One click would be a bad battery connection
Repeated clicks would be bad battery

 

And I know you said the battery was charged, but it's still worth hooking up to a running car with jumper cables to rule that out.

 

Hi Dave, My dad and I did that which got us to the point of getting the drivers side window back up and that was it.

Repeated clicking, the battery is only about 3 years old and is a Mini battery.

 

Have the battery, charging system, and starter checked. Just because it's charged and shows proper voltage doesn't mean it can hold a load. Also, the starter could be going out and drawing too high of a load. It could have caused the old battery to die, and the new battery to die quickly.

 

Did you attach the jump leads to the mini battery terminals, or the mini battery leads?

If you want to rule out the wiring in the mini as the problem, disconnect the mini battery and jump straight from your dad's car to the power leads.