I would go ahead and check your alternator voltage, could be weak. My guess is you did run the battery down possibly, and it said that because it was trying to charge the battery back up and the alternator didn't output enough. You probably have a weak alternator so it was tough for it to keep up with charging the battery and running all the electronics. You did say you replaced the alt 18months ago... I hope it isn't going! Check voltage! You can to it in engineering test mode so it's easy to do. Charging the phone shouldn't cause long term damage... Worst thing it can do if everything is working perfectly is drain your battery.
Just my guess.
2008 Mercury Sable Premier
2014 Ford Focus Electric
1997 Mercury Grand Marquis GS
Moved On: 2000 Sable LS Premium Duratec
Last edited by Sam; 11-07-2012 at 12:56 PM.