By inspecting the first example, then looking at the computed tab in Webkit's inspector, you can see the matrix the first one used was:
-webkit-transform: matrix3d(1, 0, 0, 0,
0, 0.5000000000000001, -0.8660254037844386, 0, 0,
0.8660254037844386, 0.5000000000000001, 0,
0, 0, 0, 1);
Applying this as is doesn't seem to work in your second example, but this maybe because of other differences in your code.
The reason this is used is because a rotation matrix in the X axis looks like:
[1,0,0,0],
[0,cos(a), sin(-a), 0],
[0,sin(a), cos( a), 0],
[0,0,0,1]
In your case, a is 60 degrees, which in radians is π/3. cos(π/3) = 0.5, and sin(π/3) = sqrt(3)/2 = 0.866025.