My '04 with a Cummins did that a few times a while back and got better. If I recall correctly, I could flip the switch and use the down arrows to select 2nd and all was well. It may have improved because it was lubed with the special Pac Brake lube.
For the batteries, I would put a voltmeter on them. If the batteries are old or the terminals corroded, you won't get much charge.
Be careful with the house batteries. If they are low or old, they will work the alternator hard enough to get it so hot it will fail.