The Dark Knight,
Best of five will always favor the superior player as it's a larger sample size of play. Fed's best of three clay record against Nadal is 2-5, pretty bad but better than 0-7 in best of five.
Just as Andy Roddick has 3 best-of-three wins against Fed but none in best of five.
By the way, outside of the TMC event where Fed has dominated, his best of three record against Nadal off clay is 1-3.