I didn't really think about it until you said that, but yes it does take longer to bake. I have also noticed that if I bake a chocolate and vanilla (at different times) in the same size pan, that the vanilla doesn't rise as much. Im glad you pointed that out!
Boy am I glad I ready this post - I thought I did something wrong when I baked a choc and van cake side by side in the same pan and the van side did not rise up as high as the choc side. But what could you do to prevent this I wonder???