Let $\lambda_1, \dots, \lambda_n$ be the diagonal entries of $\Sigma$; note that $\Sigma$ is invertible, and the diagonal entries of $\Sigma$ are $\lambda_1^{-1}, \dots, \lambda_n^{-1}$. Now, we can rewrite your condition on $B$ as $B-B^T = \Sigma^{-1}(B-B^T)\Sigma$.
Let $B \in M_n$. For $1 \leq i,j \leq n$, let $c_{i,j}$ be the $(i,j)$ entry of $B-B^T$. Then, the $(i,j)$ entry of $\Sigma^{-1}(B-B^T)\Sigma$ is $\lambda_i^{-1}\lambda_j c_{i,j}$. So $B$ satisfies the above equation (i.e., $B \in V$) if and only if either $\lambda_i = \lambda_j$, or $c_{i,j} = 0$.
Since $\Sigma$ is fixed, $B \in V$ is equivalent to the constraint that $c_{i,j} = 0$ for all $i,j$ such that $\lambda_i \neq \lambda_j$. In other words, for all such $i,j$, $b_{i,j} = b_{j,i}$, where $b_{i,j}$ represents the $(i,j)$ entry of $B$.
So if we let $S := \{(i,j) : \lambda_i \neq \lambda_j\}$, then a basis for $V$ would be $\{E_{i,j} + E_{j,i} : (i,j) \in S\} \cup \{E_{i,j} : (i,j) \notin S\}$, where $E_{i,j}$ denotes the matrix whose $(i,j)$ entry is 1, and whose other entries are 0. Note that the left part of this union contains $|S|/2$ elements, since each $(i,j)$ and $(j,i)$ in $S$ contributes the same matrix. So $\dim V = |S|/2 + (n^2-|S|)$.
Note that $|S|$ (and hence $\dim V$) depends not only on the number of different entries of $\Sigma$, but how many of each there are; for instance, if its entries are $1,2,2,2$, then $|S| = 6$, but if its entries are $1,1,2,2$, then $|S| = 8$.