What is the problem? I'm assuming they are too deep. I think they designed them like that for when you go on rougher terrain your drinks don't fall out.
I think you probably could line the cup holder with some card paper so it has the shape of the cup holder. Pull the card paper out and fill it with spray foam. Then cut to the depth you want and then place it back in.
Or something like this may work: http://www.amazon.com/Trademark-Shal.../dp/B0055UBMAW