This is just a guess, but it sounds like your son might be acting out from maybe a fear of what might happen to his daddy when he's out of the house.
I think, at some level, even the little ones know more, or sense more, than we think they do. Maybe, without even being able to put words to it, he knows that daddy was away and got hurt....so now, when daddy goes away he gets scared, and that fear comes out in this "bad" or naughty behavior....just to try to vent out emotions, or something.
I'm sure someone else might be able to give you a better, more professional assessment, but that is what comes to my mind. I know that when I have certain fears, my behaviors don't always match my feelings, and I respond with frustration or other "negative" behaviors.
Do you have access to some help through the VA? Maybe a child psychologist or child behaviorist? It might be helpful for your family to hear a professional opinion. Maybe you can help your son cope with his feelings in a more constructive way, and help his fears, if he has them. Also, it sure would make YOUR life easier, and be better for the whole family!
Just an idea, but I would ask around about it, if it were my family.....I'm sure maybe you have a big checklist of ideas going already, I know all the moms here have tons of good ideas!!