No BS here...
Really... try shutting your door normally. Now roll down a window and shut it. You will find a distinct difference. That is the air resistance upon the glass. When shutting the door, you are moving a huge volume of air, about 4. 5' by 3. 5' into the cab. That volume is too much to dissapate through all of the vents. There is just enough backpressure to let the door not latch all the way if it is not given enough force. Also take a look at how much the side windows pop out when the front doors are shut. I used to be a service manager, and I have also spent several years in the body shop. It is a fact that cabs without sliders will break windshields at a higher rates then cabs with a slider. How many earlier second gen Dodges were seen with a crack about 5" down from the top of the driver's side? There were lots of them back then when the price of the glass used to be $1100. The 98. 5s and up don't crack like the older ones. I think they have a little better venting systems (some of it due to the quad cab, and some to design changes I believe), which makes it harder to break the glass. Your sig does not say if you had a quad cab, so I mentioned the pressure theory.
Take your fist and hit the outside of a windshield. It won't break. Now hit the inside. Whamo, big cracks. The windshield is designed to be strong when the force is directed at the cab. It takes a lot less pressure to break it from the inside. The stress of a shutting door and the air pressure can make a crack in the glass.
GM sliders were made of plastic, and they quit making them around 99 just because they would crack the slider frame and leak in. This was due to the tightness of the cab and the shutting of the doors.
The inertia of a shutting door would cause lateral movement of a plug. Remember, you PUSH a plug IN to get it seated. To unseat it, you would push or pry OUTWARD. The plug whould not wiggle in the hole. A body plug should fit snug and not loose.
My 99 does not have plugs in the door. I assume that was a design change? I know the paintless dent repair guys will drill holes anywhere and everywhere then put plugs in them when done.
Being I have been a service manager, I am used to people being upset and difficult to deal with. It doesn't take much these days for someone to have a bad day. I don't get irate when someone is screaming at me. I am way to relaxed.
That is way I did not make a good service manager, because I was too nice and honest to customers.
Attention: TDR Forum Junkies 
or better yet I could use this as my lemon law to trade my truck in for a 2003 at DCs expense... 
