Your furnace is likely cycling the limit switch. My same furnace on my 2015 Kodiak did the same thing. I spent almost two years trying to explain to my local, selling RV dealer what was happening. He just wouldn't listen. He knew better. It was obviously over-firing, or had a hot spot near the burner that caused it to shut the burner down repeatedly until the blower cooled things down again. Annoying and could be dangerous. My dealer finally got tired of trying to fix it his way and got mad at ME because of his frustrations. He screamed at me and had me take the rig off of his lot, and told me to find someone smarter than him to fix it (not hard). I was always nice to him because I know his staff and family, so couldn't understand his meltdowns. He screamed at the factory, and ultimately lost his franchises (can't sell ANY new rigs - only used rigs on consignment and some general service). Atwood called me the day after I brought my rig home, and actually sent a tech from the factory to my house the next day - couple hundred miles. Atwood said my dealer wouldn't or couldn't tell them what the problem was, so they declined warranty payment. The factory tech was awesome, listened to my analysis, agreed, checked it, and replaced the (still under warranty) furnace with a new unit in less than an hour. He said they had issues with that model and upgraded it - and said the dealer should have know that. You might want to contact Atwood directly or work with a good dealer. Good luck.
2009 GMC Sierra 1500HD 5.3 Bells and Whistles
2015 Dutchmen Kodiak 263RLSL