If it is not a matter of doneness - as you say that you check them first, let me tell you that I recently read a thread here at cc which said that to get perfectly domed cupcakes you should preheat your oven to 400 then when you are ready to put your cupcakes in, lower the temp to 350. I have not tried this yet, but there were some rave reviews on this. Hope this helps
It also helps to add 1tsp. of baking powder to your mix, and extra flour...I have used up to 1 c. per box mix. I think that the baking powder is the key, though. Whenever I add the baking powder, I get nicely domed cupcakes.