Hi,
I don't know why they are different. 6D vs. 4D is pretty close. I used Wong's PBJA software which computes the indices using combinatorial analysis and not using computer simulation of millions of hands. I am sure either set will work just fine. I have confidence that Wong's software gives exactly the right index as predicted by combinatorial analysis. Indeed, the indices his software predicts for the Halves system directly contradict in many cases those published in his own book, Professional Blackjack!
The thing to remember is that the true value of an index is not worth very much in practical terms. For example, the most commonly used index is 16 vs. T, which is variously quoted as 0 or +1. If you play that index as +2 for your entire life the amount of EV you give up wouldn't buy a cup of coffee.
Think about it, how often do you make the decision 16-T when the count is actually between 0 and 1? So first of all, the even is extremely rare. Then, the index is the break even point between the two plays, hence right around the index you could pick one play or the other and they would be roughly even in their EV. Thus, for practical purposes, all indices are approximate, and if the value given is within 1 of the "correct value," that's good enough.
Indeed, there may be no such thing as an absolutely correct index for any play, since ultimately each index needs to be computed for every composition of your hand, various game conditions, etc.
For example, you would always hit 14 VS. T, wouldn't you? I don't even keep that index in my arsenal. But what if you are playing single deck, and your dealt 7-7? Then you stand, right? Even when the count is -1 (the two 7's and the T).
Indices are good to learn, but strategy variation is not that important to playing a winning game (especially in multiple deck), and most of the plays you make where you vary are because the count is way above/below the index.
As you can see, your question is one I have thought about before -- I just wish I had a few better analogies to really bring home the point
--Mayor