I don't have an exact answer, but we can go over some theories.
The reason dubs are made in the first place, are to increase the viewer base, so that more people can watch the show. Obviously there is a direct relation to how much money a corporation earns in merchandise, to how many people actually watch the anime.
One thing those in charge (again, due to a lack of first-hand knowledge here, there is ambiguity as to "who", but please try to overlook that) have in mind probably is how they think the varied viewer base responds to music.
Every country/ geographic location has its own style, and hence, taste in music. While I cannot directly say that the music is more "Japanese" in subs and more "American/English" in dubs, it is obvious that change in a certain style, might improve the scene. Think of it this way: If there's a scene that has different implications in different cultures, then the tone of the scene has to adjusted to fit the scene, especially if the intended tone of the scene cannot be directly translated due to a difference in culture. You can take a moment here to blame for reading too deeply into this, and not providing substantial evidence to support my statement. I can't help but accept it, but thanks for reading so far anyway. Like I said, this is more to discuss the possibilities rather than to give you the definitive answer.
Moving on, there is the possibility that the music is subject to laws. Since music is sometimes made by a third party, while a company that produces the anime may have the rights to the visuals, they may not necessarily have the right to use music that will be broadly distributed across the globe. Let's say OST Producer 1 states in the terms and agreements that this OST can be used to be broadcast in Japan. Obviously, the internationally released dub will be broadcast all across the globe, and in my limited (second-, even third-hand) experience, most leases of this sort are based within the country, i.e. the jurisdiction is within the sovereign state of so and so (in this case, Japan). So, to avoid having to come up with separate legal documents this might be the alternative.
Further, there is the possibility that the director had the choice of using more than one music piece for a scene, and wanted to wanted to use both. Hence, the sub has one, and the dub has the other. This way, the director's a initial indecisiveness is solved, and allows him/her to explore the difference different artistic choices bring about.
In general, I like to think that the original, the sub, is the attempt to capture the story, and the dub is the attempt to capture global audience. This may or may not be true, but if it is, then one can view the initial score as the one that the company wanted to roll with, and the one that appears later is a move to pander to the audience. This is more of an afterthought, and I don't think this theory holds as much weight as some of the others above.
tl;dr : To sum it all up in a phrase each:
- Cultural differences
- Legal issues
- Audience pandering (somewhat related to the first point)
I'd just like to conclude by saying, in Russia, Tili Tili Bom Bom is apparently a lullaby. If that's true, you can see what I mean by saying music in one country has a different effect than the same music in another that has evolved separately, and is uninfluenced by the same factors. Just a thought.