Microwave Butternut Squash
I suspect the problem was the 1/2 inch of water, which would have absorbed a goodly amount of the microwave energy, preventing it from heating the flesh of the squash.

For very slightly more detailed instructions, which are not too far off from what you have tried, you might try this recipe from the Food Network, which recommends 5-7 minutes for 1/2 of a squash, but no water.