This is an extended version of Wahba's Problem.
Let $R_x(\alpha)$ denote a 3D rotation matrix around the axis $x$ by an amount $\alpha$.
For given unit vectors $\{u_k\}_{k=1}^3$ and $\{v_k\}_{k=1}^3$ I want to solve the system $$ RR_{u_k}(\alpha_k)v_k=v_k, \quad 1\leq k\leq 3.$$ The variables that I can solve over are the three angles $\alpha_k$ as well as a full rotation matrix $R$. Clearly, $R=I$ and $\alpha_k=0, \forall k$ is one trivial solution. Wahba's problem arises by setting $\alpha_k=0, \, \forall k$ and then asking for the best fit of $R$ but where the RHS vector $v_k$ is replaced with $u_k$. (Wahba's also have weights).
However, numerically, I find that there are other non-trivial solutions. Using a very lengthy brute-force (analytical) method, I can establish that for the a particular choice $u_1=u_2=[1\; 0\; 0]^{\mathrm{T}}$ and $u_3=[0\; 1\;0]^{\mathrm{T}}$ there are either 2 or 4 solutions (including the trivial one) depending on the vectors $v_k$. (Other number of solutions occur for a set of $v_k$'s of measure zero).
However, I cannot crack the general case of arbitrary $u_k$'s. I feel that there could be an elegant geometric argument.


This is a bit too long for a comment, but not quite an answer.
Here's a way to reframe the problem. Let $w_k$ denote the unit-vector in the direction of $u_k \times v_k$, so that $$ R_{u_k}(\alpha) v_k = \cos (\alpha) v_k + \sin(\alpha) w_k. $$ Thus, the equation of interest becomes one of solving $$ R(\cos (\alpha_k) v_k + \sin(\alpha_k) w_k) = v_k, \quad k = 1,2,3. $$ To put this another way, we're looking for a solution to the matrix equation $$ R \pmatrix{v_1 & v_2 & v_3 & w_1 & w_2 & w_3} \pmatrix{ a_1\\&a_2\\&&a_3\\b_1\\&b_2\\&&b_3} = \pmatrix{v_1&v_2&v_3}, $$ subject to the constraint that $R$ is rotation matrix and $a_k^2 + b_k^2 = 1$ for $k = 1,2,3$.
Let $V = [v_1 \ \ v_2 \ \ v_3]$. If the $v_i$ are ordered such that $\det(V) = 1$, then $V$ is a rotation and we can substitute $S = V^{-1}R$ to get the equivalent equation $$ S \pmatrix{v_1 & v_2 & v_3 & w_1 & w_2 & w_3} \pmatrix{ a_1\\&a_2\\&&a_3\\b_1\\&b_2\\&&b_3} = I $$