Just got the MSP16 reflash at the dealer and now my iPod (using AudioLink connector) doesn't auto pause when I shut the car off (just keeps playing, which could run down the battery if parked for an extended period of time) and sometimes when I start the car the HU will be off, when it was on when I shut the car off.

Is there anyone who's had the MSP16 reflash and is also using the AudioLink for their iPod? Could the reflash cause this problem?

I fixed this by disconnnecting the battery which reset the HU. All is normal again. Thanks to the RPMstore for the suggestion.