Actually on thinking about it, it doesn't make sense.
When the new Top Gear started, I could see Clarkson getting that much because the show was going to depend on him to get going again. But Richard was the newboy, and even in the 2003 series when James came along, the new series wasn't exactly an institution yet. So why would Richard be being paid a lot more than James at this point?
On a slightly different point, do the presenters get payments from the repeats on UKTV G2 and BBC Three? IF so, even James should be minted from those!