I'm a little bit confused by your notation (the periods specifically. do they represent subscripts?).
But I believe the only substantive difference in the two equations is that S is the spin operator i.e. the physical observable which generates rotations around some axis while ##\sigma## is a Pauli spin matrix which is proportional to the representation of the spin operator in the spinor representation of the rotation group.
[tex]J_n \to S_n= \frac{\hbar}{2} \sigma[/tex](and ## h = 2\pi \hbar##.)
So you could just as aptly have written ## S_.n X = \frac{h}{4\pi} X##.
So for example in the spinor representation (in the spin-z operator's eigen-basis):
[tex]J_z \to S_z = \frac{\hbar}{2}\sigma_z=\frac{\hbar}{2}\left(\begin{array}{rr} 1 & 0\\0 & -1\end{array}\right)[/tex] while in the vector representation (say of a massive boson) you have:
[tex]J_z \to \hbar\left(\begin{array}{rr}1 &0 &0\\ 0 & 0 & 0 \\ 0 & 0 & -1\end{array}\right)[/tex]
Here the ##J_z## is the physically interpreted operator representing the observable for z-component of spin in any representation. ##S_z## is (I believe in most texts) specifically its spinor representation and the half of Plank's constant factor is factored out to give the more purely mathematical Pauli spin matrix.