Bubbling around marble sills?

Hi All - We moved into our first home 10 months ago (December 2009) and did a complete interior paint job using latex paint. Unfortunately during a recent storm a tree fell and struck our house, and as a result, it led me to do a complete top to bottom inspection to look for damages.

I was looking at the window in my bedroom (away from the area of the tree strike) and noticed in the bottom left corner of the marble window sill there was a 2 inch by 1 inch bubble in the paint. I was able to push the bubble and it flexed back to the ball and came back out. I immediately inspected the other windows and found the same issue at the other window in my bedroom in the front of the house, and a window in my living room (downstairs) at the rear of the house.

I used a pin to open the largest of the bubbles fearing moisture damage, and the paint peeled away, along with the thin top layer of plaster (we have plaster walls throughout the house - which is 50 years old). Thankfully the wall wasn't damp. I wanted to ask though, if this is common for paint to bubble beneath marble window sills (I'm not sure if it's caused by the sill sweating, or the change in temperature). It's quite possible the bubbles have been there for months, as it was very hard to recognize. I don't believe that it was caused by the tree strike, but still want to find the root of the problem and then patch the paint (there isn't any caulking between the sill and the wall, which led me to believe that the sill may sweat and the moisture would soak into the wall).

Any ideas or tips? Thanks!

The only time I have seen bubbling is when you attempt to paint latex paint over oil base paint, without the use of a good quality primer or you are absorbing moisture into the drywall, and the latex paint is not allowing it to dry out. You really need to surgically remove the paint and inspect the drywall to find the cause of your problem.