That is where you are making your mistake. You are looking at the potential total number combinations which would be 6 squared (6 numbers, 2 dice) exceeding the potential combinations of 2, 3, 3 and 4. However, the initial hypothetical was based upon a single number between 3-6 and not the total of two dice.
Actually, the values in my grid do not represent a total. naaman defined win as "if you roll two dice and need at least one (both are not necessary) to come up three or better". The W in my grid represents this win criteria (at least once die rolled a 3,4,5,6).
Here's yet another way to calculate the probability...
You roll both dice and want to determine if you won. You look at D1 first:
1 -> need to look at D2
2 -> need to look at D2
3 -> win
4 -> win
5 -> win
6 -> win
2 -> need to look at D2
3 -> win
4 -> win
5 -> win
6 -> win
So we can say...
4 out of 6 times you win regardless of D2's outcome, but
2 out of 6 times you need to look at D2 (which we know has a 4/6 chance of winning)
2 out of 6 times you need to look at D2 (which we know has a 4/6 chance of winning)
... which is equivalent to ...
4/6 +
2/6 * 4/6
2/6 * 4/6
... which is 8/9 or 88.89% (the same outcome as my grid).