I've been having trouble with the choice commonly used to name the elements of the scattering matrix in quantum mechanics. Let's say we are dealing with a simple potential barrier in 1D, such that if we fix the energy the only two possible states far from it are those with right moving ($k>0$) and left moving ($-k>0$). Given an incoming state, the scattering matrix gives the outgoing state:
$|\psi_{out}\rangle = S|\psi_{in}\rangle$
where we can restrict ourselves to states of the form:
$ |\psi_{in}\rangle = a|k\rangle + |-k\rangle $
If the incoming state is just $|k\rangle$, then I might define the reflection $r_k$ and the transmission $t_k$ such that $|r_k|^2$ is the probability that the system has been reflected (that the final state is found in $|-k\rangle$) and $|t_k|^2$ is the probability to be transmitted (that the final state is found in $|k\rangle$):
$ |\langle -k|S|k\rangle|^2 = |r_k|^2 \qquad |\langle k|S|k\rangle|^2 = |t_k|^2$
Similarly for $r_{-k}$ (I'm not assuming yet time-reversal, so these coefficients may be different from the one above for now):
$ |\langle k|S|-k\rangle|^2 = |r_{-k}|^2 \qquad |\langle -k|S|-k\rangle|^2 = |t_{-k}|^2$
This implies that, up to a phase:
$ \begin{cases} S|k\rangle = r_k|-k\rangle + t_k|k\rangle\\ S|-k\rangle = r_{-k}|k\rangle + t_{-k}|-k\rangle \end{cases} $
(I know this is not the way to define it, but I just want to place the elements of $S$ in the right place, not compute their values)
Therefore, in matrix representation:
$ |k\rangle = \left(\begin{matrix} 1\\ 0 \end{matrix}\right) \qquad |-k\rangle = \left(\begin{matrix} 0\\ 1 \end{matrix}\right) \qquad S = \left(\begin{matrix} t_k & r_{-k} \\ r_k & t_{-k} \end{matrix}\right) $
However I believe the standard representation for the S-matrix (and the one used by my professor) is:
$ S = \left(\begin{matrix} r_k & t_{-k} \\ t_k & r_{-k} \end{matrix}\right) $
with the same representation for $|-k\rangle$ and $|k\rangle$. What is wrong with my reasoning? Why is it different? Was it a computation error? Or am I looking at reflection and transmission from the wrong side? I can't figure it out.