First off to House Repair Talk and congrats on your home purchase!
Was the "bubbles" there when you bought the house?
Are you sure it's water damage? I don't see any water marks. To me, from my computer chair, it looks like a bad tape and mud job, but I could be wrong.
Have you noticed any wet spots on the floor after a rain?
If you get a ladder, you can water test it with a water hose. Spray at the bottom of the skylight curb and slowly work you way up. Be careful on the roof, gravity ALWAYS win.