Ours has had bubbles from day 1. Depending on the weather, sometimes they are gone/minimal, other times they are there. Last year at the Goshen Rally, I asked the rep from the company about the bubbles. Apparently the roof isn't glued down across the entire roof. He said some bubbles are normal, and if they really bothered me to use something that won't poke a hole in the rubber, and work the bubble towards a vent or something, the caulking would have to be "broken" to allow the air to escape, then re caulked. So far I haven't done this, as it hasn't become an issue yet.