[kdog_x]

So after sitting in traffic for about three hours this morning when I shut the car off I get the charge battery warning. I came back after a couple hours, car starts just fine, no warnings or anything. Then when I shut it off 30 min up the road I get the charge battery warning again.

The battery is less than two years old, (probably closer to a year) and has about 40,000 miles on it. Does it sound like maybe the alternator is going out? I'm currently about 200 miles from home, and won't be back for a couple days, so hoping I won't come out to a dead vehicle!

I have a multimeter with me. The battery reads 14.6 V while it's running. And then looks like it drops to 12.5 when it's off for a little bit. Doesn't seem to out of line to me, so I'm not sure why I'm getting these warnings

[Enabled]

Yea, I would monitor how it's charging and holding voltage. 12.5 is on the low side, especially right after running. Typically a good charged battery is 12.6-12.7V.
If alternator is putting 14.2+, then it it doing its job. It's variable, and when the battery charge is good, it will charge only when decelerating. However when battery is low, it will charge at all times.

I assume you registered the battery at last change?

It could be a dead cell in this battery.

Any dde codes? Dde controls alternator via a minor network, which can set codes if it's not running right. Hopefully those codes weren't blocked by tune. I've seen a few tuners that block way more than needed DTCs.

[kdog_x]

The battery was registered with ISTA when replaced. Not sure if there's codes, I'm on the road so I can't check.

3 stops so far and it's still starting ok. Guess I'll have to give it a long charge when I get back and have it load tested if it still has issues.

[kdog_x]

I never understood the whole "charge while decelerating" thing. I see the indicator on the dash go into charge mode, but wouldn't the battery always charge if the alternator is applying 14.6 volts to it?

I recall when the battery had issues last time, every time I would get into the car it would say that all of the electrical devices were shut off. It would also disable the keyless entry and I would have to use the key fob. Strange thing is, it's not doing that. The keyless entry still works, no messages when I get in the car, only when I shut the car off after driving do I get the charge battery message. Maybe it's a dead cell like you suggested. I head back home today, so I'll give it a good long charge overnight and see how things look.

[Enabled]

It's a variable alternator. It reduces chargin capacity to low 13 Volts when it is not needed.