BATTERY NOT CHARGING = Bad Alternator (for me, anyway)
I realize this post is several years old, but I wanted to contribute to the anyone else who might be running into this same issue.
I had the same problem. Instrument cluster started reading "BATTERY NOT CHARGING" Friday morning, but if I starting driving, once the engine got up to around 2000RPM, the light would go out. It didn't do it the rest of the day. But Saturday, when I started looking into the issue more, the message would almost never go away.
I did everything that I could find in the way of testing, short of taking the battery and alternator in to have them tested, since this is my only transportation; 2003 TB SWB with 213K miles. I think this was the original alternator. I usually keep all of my receipts and could not find where it had been replaced. I bought it in Nov. 2007 with 54K miles on it, so it could have been replaced before then, but it still lasted a long time.
I checked the cables to make sure they were not corroded. I checked the battery voltage before and after starting. Before starting the engine, the voltage was around 12.2V. After starting, the battery voltage would drop to 11.7 and continue to drop slowly afterwards until the alternator kicked in, then the voltage would go up to 14.4V. Problem was, the time it took the alternator to kick in varied.
So, I charged the battery up and drove 11 miles into town to AutoZone. I normally go to Advance Auto Parts, but AutoZone was the only place with a lifetime warranty on the alternator, except for Rock Auto, but I didn't feel like I could wait for the part to arrive.
I've suspected the alternator had been going bad for some time. Even though everyone says not to trust what the volt gauge on the dash, it would always fluctuate between 13.5-15.5V. After changing the alternator, the needle stays at 14.5V.
I've read many posts that say, when the engine is cold and it is cold outside, that the "BATTERY NOT CHARGING" message is normal; it is not normal. There is a problem and it should be addressed sooner rather than later. I've also read that a lot of people have only cleaned the throttle body to get rid of the error. I just don't see how this is possible. It might fix rough idling issues, especially when using the A/C, but fixing this issue is a stretch. It should probably be done in conjunction with replacing the alternator or any time the battery is disconnected for more than 20-30 minutes, if it has not been done recently.