The Ceiling Debacle

I'm still working on the drawers for the dresser. My mistake last week was putting the varnish on outside, in the humidity. Four days later it still hadn't really dried. We brought them in Thursday night and miraculously, they were ready for another coat of varnish by Friday night. This morning I got up and put on a third coat, and they should be ready to put back in the dresser tomorrow. This has also allowed the chalk paint to have plenty of time to cure. A small bonus. 

I decided to tackle the ceiling this weekend. Mainly because there isn't a lot I can get done in the room until the ceiling is repainted. 

Here is the almost blank slate I'm working with:

This is the view of the room from his door. The closet is to your right. It currently has the dresser, his desk, and his bin-o-stuff in it so I can paint. From this angle, the carpet doesn't look too bad. Sadly, that's far from the truth. Also, the walls were refreshed with paint three years ago, but this boy is apparently very hard on his room, and it looks dingy and gross. You can also see the water damage up above the window. Here's a close up:

This morning, after we cleared everything out of the room, I was really confident I would just put on a coat of primer, let it dry, and then paint the ceiling. What cold be simpler?

6 hours later and three coats of primer later, here is what I'm still dealing with:
It's....better. But it's not fixed.  And it certainly doesn't look like I've painted on three coats of primer! I'm going to put on yet ANOTHER coat here in a few minutes and hope that does the trick. Seriously, it was just a leaky tube that allowed water to drip onto the ceiling. Why the Zinser primer isn't covering these spots completely is the burning question right now. So back upstairs I go to paint on primer. Again...