I like my cupcakes flat, but here's a tutorial that might help you. Are you doing the rising the temperature and then lowering the temperature thing?
http://www.cakejournal.com/archives/cupcake-decorating-part-2
imagenthatnj is correct, start the cupcake at a higher temperature, 400 degrees F for a few minutes. Once you see the dome starting to form drop the temp back to 350 degrees F. I also suggest you fill the cups a little higher if you like a nice full domed top.
Mixes are formulated for certain effects, so perhaps the mixes you use are intended to bake flat cupcakes. With that in mind you could add a pinch more leavener to boost the dome.
I recently discovered its the higher temp. I usually bake cakes on a lower temp, and they bake flat...so my cupcakes do the same. Baked cupcakes at my grandma's house recently and her oven runs hot (I found) and the cupcakes had a gorgeous dome on them instead of flat...same recipe (doctored box) and same pans...only variable was oven temp.
AI disagree on the homemade thing. I've made scratch cake recipes before and they've come out flat too. I believe it's the temperature trick. :)
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