Do the cup cakes bake faster in a 24 hole cup cake tray rather than a 12 hole cup cake tray?
I immediately thought of this table, from the front of the muffin section in Bread, by Beth Hensperger*:

Muffin size          Baking time     Yield
Mini/gem (1 5/8")    10-15 minutes   18-20
Regular (2 3/4")     20-25 minutes   9-10
Oversized (3 1/4")   25-30 minutes   6-7
Muffin cake (8-9")   55-65 minutes   1


The baking times are for 375-400F; most recipes will fall around that range. Note that the yields don't necessarily match up to typical pan sizes; for example, if you take a recipe meant for 12 regular muffins, you'll probably have more batter than you need for a pan of 6 oversized muffins. Similarly, if your recipe says to bake regular muffins for 30 minutes, you might have to bake miniature ones a bit over 15 minutes. "Muffin cake" refers to baking in an 8-9" pan of some sort - the author says that you can get away with it for any muffin recipe, but I've never tried it!

P.S. I know this is for muffins, but cupcakes are fairly similar, so I think it'll be about right!

* At least, I'm pretty sure it is. I have a copy of just this page (for the recipe next to the table, actually), from a book my mom has. I recognize the cover, I know we had that book, I think this was in it, and Google book search somehow found it when I searched for "fresh-lemon muffins".