I guess I wasn't clear of the issue I am having. When I enter my vehicle my phone starts playing music, it doesn't actually play through the sync system. The sync system plays whatever I had it on last, which is what it's supposed to do like you said. When I enter the vehicle and start it up, my phone shows that music is playing, the music is not playing through bluetooth audio. I have to go into the iPod app and stop the player. This happens no matter what sync is playing, cd's, USB, or SAT radio, my phone starts to play music no matter what. Also because my phone automatically connects to sync, when the iPod is playing you can't hear it from the phone or truck until you physically tell sync to play bluetooth audio. No sounds come from the phone when connected to sync.
As for your question about the windows being down. I was referring to the comment that sync never works. The only time I have trouble with sync is when the windows are down and it doesn't recognize voice commands due to background noise.