$\DeclareMathOperator\SO{SO}$Set \begin{equation} \begin{aligned} \Gamma_1 &= \left\{ I_{6}, \; \gamma_1:= \left( \begin{smallmatrix} 0&1\\ 1&0 \\ &&0&1\\ &&1&0\\ &&&&1 \\ &&&&&1 \end{smallmatrix} \right), \; \gamma_2:= \left( \begin{smallmatrix} 0&1\\ 1&0 \\ &&1&&&\\ &&&1&&\\ &&&&0&1\\ &&&&1&0 \end{smallmatrix} \right), \; \gamma_3:= \left( \begin{smallmatrix} 1&&&\\ &1& \\ &&0&1&\\ &&1&0\\ &&&&0&1&\\ &&&&1&0 \end{smallmatrix} \right) \right\}, \\ % % % \Gamma_2 &= \left\{ I_{6}, \; \gamma_1':= \left( \begin{smallmatrix} 0&1\\ 1&0 \\ &&0&1\\ &&1&0\\ &&&&1\\ &&&&&1 \end{smallmatrix} \right), \; \gamma_2':= \left( \begin{smallmatrix} 0&&1&\\ &0&&1 \\ 1&&0&\\ &1&&0\\ &&&&1\\ &&&&&1 \end{smallmatrix} \right), \; \gamma_3':= \left( \begin{smallmatrix} 0&&&1\\ &0&1 \\ &1&0\\ 1&&&0\\ &&&&1\\ &&&&&1 \end{smallmatrix} \right) \right\}. \end{aligned} \end{equation}
I was able to prove that $\Gamma_1$ and $\Gamma_2$ are not conjugate in the special orthogonal group $SO(6)$, that is, there is no $a\in SO(6)$ such that $a\Gamma_1a^{-1}=\Gamma_2$. However, the proof is quite involved.
Do you have a simple argument to prove that $\Gamma_1$ and $\Gamma_2$ are not conjugate in $SO(6)$?
My interest in the pair of group is that they almost conjugate, that is, there is a bijection between the groups that preserves $SO(6)$-conjugacy classes. This follows easily since the eigenvalues of any non-trivial element are $+1$ with multiplicity $4$ and $-1$ with multiplicity $2$.