When you talk about the eigenvalues of $A^{(2)}$ over $V^{(2)}$, you assume that the image of $A^{(2)}$ lies within $V^{(2)}$ (or, in other words, that $V^{(2)}$ is an invariant subspace of $A \otimes A$). Note, however, that this is not generally the case. For example, we can consider the map $A$ over $\langle x_1,x_2 \rangle$ defined by
$$
Ax_1 = Ax_2 = x_1
$$
or in terms of matrices, $A = \left(\begin{smallmatrix}1&1\\0&0\end{smallmatrix}\right)$.
Note that $A^{(2)}(x_1x_2) = x_1x_1 \notin V^{(2)}$.
Because $A^{(2)}$ (as restricted to $V^{(2)}$) is not an endomorphism, it doesn't make sense to talk about its "eigenvalues".
Suppose that $A$ permutes the vectors $\{x_i\}$ by some permutation $\sigma \in S_n$. That is, $Ax_i = x_{\sigma(i)}$. For convenience, let $x_{ij} = x_ix_j$.
Note that $A^{(2)}$ is itself a permutation of the basis vectors $\{x_i x_j:i<j\}$. In particular, we have
$$
A^{(2)}:x_{ij} \mapsto x_{\sigma(i)\sigma(j)}
$$
Ultimately, the eigenvalues depend on the cycle decomposition of this new permutation. This depends only on the cycle decomposition of the original permutation.
For example: suppose that $A$ is the map
$$
x_1 \to x_2 \to x_3 \to x_1\\
x_4 \to x_5 \to x_4
$$
That is, $A$ has the cycle decomposition $(1 2 3)(45)$. Then $A^{(2)}$ can be written out as
$$
x_{12} \to x_{23} \to x_{13} \to x_{12}\\
x_{45} \to x_{45}\\
x_{14} \to x_{25} \to x_{34} \to x_{15} \to x_{24} \to x_{35} \to x_{14}
$$
If we were to list the elements of $\{x_{ij}:i<j\}$ in lexicographical order, we could rewrite the above as
$$
1 \to 5 \to 2 \to 1\\
10 \to 10\\
3 \to 7 \to 8 \to 4 \to 6 \to 9 \to 3
$$
So that the new permutation has the cycle decomposition
$$
(1 \;5\; 2)(3\; 7\; 8\; 4\; 6\; 9)(10)
$$
So, we're looking for the eigenvalues of a permutation that decomposes into one $3$-cycle, one $6$-cycle, and one $1$-cycle. Our eigenvalues will be each of the roots of $\lambda^3 = 1$, each of the roots of $\lambda^6 = 1$, and each of the roots of $\lambda = 1$.
Edit: assuming $x_i,x_j$ are eigenvectors of $A$.
– bartgol Aug 19 '15 at 21:07