are your windows on the outside framed with 1 x 4's mitred around them? If this is yes, then I would think that the top of the 1 x needs a drip edge or re caulking.
If not, then some how water is getting in behind the siding and into the window interiors.
This is puzzling because MOST windows have a nailing flange all around the window frame that is used to fasten the window to the frame. Then the siding goes over this.
Your leak might be higher up on the wall and finding a way to just dump out in the window.
I would wait for a good drying day and do some exploratory look sees and determine what is happening.
The paint is bubbling because the water has loosened the footing of the paint to the surface of whatever. This means that the surface has been saturated with water. This also MIGHT be a mold breeding ground in the future.
Just hard to say.
You know, then too, since this was one of those 100 year rains, maybe since it has not leaked before, it will have been just a fluke, but I would pay attention to the wet areas.