First of all sorry for my English. I've built a playhouse for my kids:

I've painted it using this:

The construction took me maybe more than 3 months (this was my first attempt to cut a wood and build something with it) and many times it rained before I could able to paint. However there was nothing wrong about the floor, before its being painted. I've waited for a moment that at least 4-5 days it didn't rain and feel confident enough that its dry enough to start painting. After ~1 week I've painted, the rains start again; and after a while I've realized that the floor was swollen like this:

I was thinking that the paint would seal the wood from water, so there would be no such problems. Actually I have no idea why this happened. I'm not sure the wood is wet or not, and this problem is because of being wet.

The floor has two layers. The upper layer is molded board (as seen in the picture) of about 1 cm thickness. The lower layer consist of boards of 2cm x 20cm x with of the entire floor. And this lower layer boards have a 0.5-1 cm space between them and they are sided perpendicular to the upper layer. I mean they are not on the same direction. So I don't expect this problem is caused because of the lower layer. Also I saw no problem when I look from the bottom.

The upper, swollen floor layer has been screwed on every beam. This picture shows the places of the beams (the view direction is from ground to the sky)

My questions:

• What might be the reason for this. Can it be the paint? Should I had used a varnish?

• Is there a way to fix it? I've tried to put some screws on the
  swollen parts, but it did not help at all. I'm 130 kg and the swollen parts are not effected when I jump on them.

Edit

Layers: Bottom View - The two layers are screwed to every beam shown in this photo: The problem: The upper layer boards are like these:

I hope its more clear with these photos.