This question arises after reading through several Stack Exchange posts and after a long chat with another user in a previous question I asked about this topic. The following "contradiction" seems to occur with the following conventions and definitions:
1.
Let $V$ be $n-$dimensional $\mathbb{R}-$vector space with a basis $(e_\mu)_{\mu=1, ... , n},$ and let $V^*$ be the dual vector space with the dual basis $(e^{* \nu})_{\mu=1, ... , n}.$
Let $$M = e_\mu M^\mu_{\ \ \nu} \otimes e^{* \nu} \in V \otimes V^{*} \cong {\cal L}(V;V)$$ be a linear map from $V$ to $V.$ We use the North-West South-East convention for the position of the indices on $M^\mu _{\ \ \nu}$.
Let $$M^T = e^{*\nu} (M^T)_\nu^{\ \ \mu} \otimes e_{\mu} \in V \otimes V^{*} \cong {\cal L}(V^*;V^*)$$ be the transposed linear map from $V^*$ to $V^*.$ We use the South-West North-East convention for the position of the indices on $(M^T)_\nu ^{\ \ \mu}$.
Let $$g =e^{*\mu} g_{\mu \nu} \odot e^{*\nu} \in \mathsf{Sym}^2 V^{*}= V^{*} \odot V^{*}.$$ be an (indefinite) metric, i.e. an invertible element in the symmetrized tensor product.
Reference: Why is not ${(\Lambda^T)^\mu}_\nu = {\Lambda_\nu}^\mu$?
2.
$$(M^T)_{\mu}^{\ \ \nu} := M^{\nu}_{\ \ \mu}$$
References: Why is not ${(\Lambda^T)^\mu}_\nu = {\Lambda_\nu}^\mu$? , Transpose of (1,1) tensor
3.
$$M^\mu_{\ \ \nu} := g_{\mu \alpha} g^{\nu \beta} M^{\alpha}_{\ \ \beta} $$
Edit: This reference to a stackexhange question no longer exists. This step is in error.
4.
$$ g_{\mu \alpha} g^{\nu \beta} M^{\alpha}_{\ \ \beta} = M_{\mu}^{\ \ \nu}$$
5. Combining 2, 3, and 4 yields
$$M^{\nu}_{\ \ \mu} = M_{\mu}^{\ \ \nu}$$ Which doesn't seem like it is always true.
Edit: After looking at the replies, I think I can summarize my confusion as follows (this may be helpful for others):
There exists the metric and the inverse metric $$g: V \to V^*$$ $$g^{-1}: V^* \to V$$
Suppose we have a linear transformation $M: V \to V.$ There exists a set of four naturally associated linear transformations: $$M: V \to V$$ $$(g \circ M): V \to V^*$$ $$(M \circ g^{-1}): V^* \to V$$ $$(g \circ M \circ g^{-1}): V^* \to V^*$$
These are the maps one obtains by applying the metric to lower/raise indices. However, given $M$, there also exists another naturally associated linear map, the transpose. As explained in J. Murray's answer, the proper way to view the transpose is as a map $M^T: V^* \to V^*.$ This gives us four new *distinct *maps: $$M^T: V^* \to V^*$$ $$(g^{-1} \circ M^T): V^* \to V$$ $$(M^T \circ g): V \to V^*$$ $$(g^{-1} \circ M^T \circ g): V \to V$$ It turns out that $(g^{-1} \circ M^T \circ g): V \to V$ is the adjoint $M^{\dagger}$. In general though, these four new maps are different than the previous four, and this is where things got confusing for me. Things get particuarly interesting if we think of $M$ as a type $(1,1)$ tensor. In this case, there are three other "naturally associated" type $(1,1)$ tensors - but all of them are different!