The only anomaly here is the low voltage you observed on the highway. I wouldn't expect that.Same here....I have the digital voltmeter as one of my gauges in the lower right corner and noticed a couple times it's dipped. Scared the crap out of me, especially since this is my very first experience with a vehicle that has this type of system. Pulling up the actual digital readout on the screen it was 12.6-12.8 and stayed like that a couple times while driving at highway speed.
I know when I wait in the school pickup line for my daughter, I turn my truck off and on a couple times while in line (because I could be waiting there 45mins + sometimes and I'm not letting it idle for that entire time). That wouldn't have anything to do with it maybe?
Either way, it's been fluctuating between 13.8-14.1 lately.
Otherwise, it sounds to me like it's charging properly. If you're doing a lot of idling, the system isn't going to charge as well because (1) it's spinning slowly, and (2) it'll get very warm. If you shut the truck off, it might cool down the engine and BSG a bit, but you're likely to be working the already-partially-discharged batteries harder (especially if you continue to listen to the radio and/or run other accessories).