... the volts on both the batteries when the engine was off was around 12.41 and stayed at 12.41 after the engine was running. so, it doesn't appear that the batteries are charging but could that be because they don't need to be charged?
No.
The alternator puts ~14 volts onto the battery terminals at all times. If the batteries don't need charging, they won't draw any
current, but the battery terminal
voltage is essentially the same whether they need charging or not.
Lead and acid, like all other chemicals, react more quickly in the heat and more sluggishly in the cold. To counteract this effect and make sure batteries get properly charged, they're given more voltage when they're cold and less when they're hot. The adjustment is pretty significant – about –22 millivolts per °C – which means that 15.0 volts is quite normal during a severe cold snap in wintertime and 13.0 volts might be adequate if the battery's unusually hot.
The one exception seems to be glow plugs. From what I piece together, (I haven't used my direct line into Ford Engineering) the glow plugs can't tolerate 14 or 15 volts for long. To prevent premature glow plug failures, they keep the battery buss voltage down while they're on by turning off one of the two alternators in the dual-alternator configuration, and by exploiting voltage sag in the single. (apparently, the single alternator can't supply the engine load, the hotel load, the glow plugs and charge the battery all at the same time) If this is true, installing a higher-capacity single alternator will cause premature glow plug failure by bringing the battery buss voltage up immediately. The difference between 12 and 15 volts may not seem like a lot, but it means 55% more heat being dissipated by each glow plug.
... Contrary to some opinions, the alternator run with no load will not hurt the diodes as there is no draw being placed on them. The regulator on the other hand can run wide open without a load degrading it's life. This is why some say no load on the alternator will immediately kill it. The statement is true only if the regulator is part of the alternator and has already suffered prolonged damage. ...
There is another condition, called “load dump”, in which no load on the alternator will damage things. When the alternator is running hard and the load is suddenly removed, (such as removing the battery while the engine's running, or disconnecting jumper cables while the dead battery's still taking a large charge) the battery buss voltage may briefly spike because the alternator doesn't turn off as fast as a load can be disconnected. This is mainly a problem in older vehicles (~1980s-1990s) because we learned how load dump behaves and how to protect against it.
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A shorted cell in one battery can also cause these symptoms, and can cause the other battery to eventually fail by denying it a full charge.
To diagnose it:
Completely disconnect both batteries from the vehicle and from each other.
Charge each one independently with a 3-step (bulk, finish, float) digital electronic battery charger.
(if you can spend $160,000 on a truck, you can spend $160 on two battery chargers)
After each charger switches to float mode, let it charge for one more hour.
Disconnect the chargers and let the batteries sit quietly for two hours.
Measure the terminal voltages. They'll be between 12-13 volts if all's well and between 10-11 volts if there's one shorted cell.
This same test can be done with an antique battery charger (the kind with a big, heavy 60-Hertz transformer that's not widely acknowledged as an "antique" just yet) but it'll take twice as long and be half as reliable. If you have this kind of charger, the procedure's slightly different:
Charge the battery until the charger's ammeter doesn't move for two hours.
Manually switch the charger to the float setting and charge for two more hours.
Disconnect the charger and let the battery sit quietly for four hours.
Measure the terminal voltage as before.
Repeat with the other battery.
Using a large fast charger won't save much time, if any. It's still necessary to to allow the battery time to come to equilibrium during the finishing charge, again during the float charge, and again during quiescence. A 10 or 20-amp three-step electronic charger will often be as fast as a 50 or 100-amp fast charger, particularly if you have low line voltage or a long extension cord. (in which case, the fast charger will
never bring a battery to 100% state of charge)
Whenever a pair of batteries has been deeply discharged – alternator failure, engine wouldn't start, left the lights on, whatever – it's a good idea to separate them and charge & test each one independently. It's not essential that they match in age or CCA capacity, but it is essential that a failed battery be removed.
When a shorted cell occurs, it's only necessary to replace the battery which has failed. Unless you neglected to notice the problem for a very long time (a year or so) the other battery will usually be fine after being topped off with distilled water, (even if it's labeled "maintenance-free") fully charged, float charged and equalized.
