OP's question is a good question. Of course, the short answer is simply "matchups." Even though the Big 4 are all, overall, better than Berdych, why would we expect them all to do exactly the same against him? Players bring different things to the table, even if they play the same general game style.
Fed - I think it's been answered correctly by a lot of posters. Fed doesn't play the type of defense that Nadal and Djokovic do. Berdych has a big game, which gets Fed away from dictating the points - he feels pressured, rushed, and goes for more than he would against a different opponent. Thus, he makes more errors. Plus, by this point, Berdych is probably simply more comfortable vs. Fed than the others and that little bit of extra confidence helps him hit out and simply play better. And, he does have tangible weapons.
Nadal/Djokovic - it's the defense. Again, Berdych is great, but like all big hitters, can be streaky. Nadal and Djokovic are so adept at running balls down, making Berdych hit another shot, that they can simply wear him down. He'll start missing. Plus, don't forget that they both have great passing shots and can go on the offensive themselves. But, instead of just "going for it" because they feel pressued like Fed sometimes does, they do more classic defense to offense, where they make Berdych get balls back, Berdych eventually puts something short back, and Nadal and Djokovic will take their opporunity.
Murray - he does a lot of what Nadal and Djokovic do in terms of defense, yet Berdych does better against him than the others. Why? It's probably just intangibles. I'm thinking that Berdych likes Murray's ball better than Nadal's or Djokovic's - the ball flight, the arch, etc. Murray often hits his backhand pretty flat and his forehand, if not actually flat, is often hit at a low trajectory, and I think Berdych likes that and feels more comfortable with that, even though, in theory, being as tall as he is, he shouldn't be too bothered by higher balls. Also, generally, Murray doesn't play defense from as far back as Nadal and Djokovic and can be a little more susceptible to a particularly hard, deep shot from Berdych changing the dynamic of a point from neutral or Murray being "ahead" in the point to Berdych being ahead in the point.