From Robert Z's answer, we have
$$\frac{m^2+n^2}{mn(m^2-n^2)^2}=\frac{1}{2mn(m+n)^2}+\frac{1}{2mn(m-n)^2}.$$
Hence, the required sum
$$S=\sum_{\substack{{m,n\in\Bbb{N}_1}\\{m\neq n}}}\frac{1}{mn(m^2-n^2)^2}$$
can be split into two parts:
$$S_1=\sum_{\substack{{m,n\in\Bbb{N}_1}\\{m\neq n}}}\frac{1}{2mn(m+n)^2}=\sum_{m,n\in\Bbb N_1}\frac{1}{2mn(m+n)^2}-\sum_{n=1}^\infty\frac{1}{8n^4}$$
and
$$S_2=\sum_{\substack{{m,n\in\Bbb{N}_1}\\{m\neq n}}}\frac{1}{2mn(m-n)^2}=\sum_{\substack{{m,n\in\Bbb{N}_1}\\{m>n}}}\frac{1}{2mn(m-n)^2}+\sum_{\substack{{m,n\in\Bbb{N}_1}\\{m< n}}}\frac{1}{2mn(n-m)^2}.$$
Let's look at $S_2$ more closely. The first summand satisfies
$$\sum_{\substack{{m,n\in\Bbb{N}_1}\\{m>n}}}\frac{1}{2mn(m-n)^2}=\sum_{m,k\in\Bbb{N}_1}\frac{1}{2m(m+k)k^2},$$
where $k=m-n$. The second summand satisfies
$$\sum_{\substack{{m,n\in\Bbb{N}_1}\\{m>n}}}\frac{1}{2mn(m-n)^2}=\sum_{n,l\in\Bbb{N}_1}\frac{1}{2(n+l)nl^2},$$
where $l=n-m$. Therefore, we can rename the dummy variables and get
\begin{align}S_2&=\sum_{m,k\in\Bbb{N}_1}\frac{1}{2m(m+k)k^2}+\sum_{n,l\in\Bbb{N}_1}\frac{1}{2(n+l)nl^2}\\&=\sum_{m,n\in\Bbb{N}_1}\frac{1}{2mn^2(m+n)}+\sum_{m,n\in\Bbb{N}_1}\frac{1}{2m^2n(m+n)}.\end{align}
So,
$$S_2=\sum_{m,n\in\Bbb{N}_1}\left(\frac{1}{2mn^2(m+n)}+\frac{1}{2m^2n(m+n)}\right)=\sum_{m,n\in \Bbb{N}_1}\frac{1}{2m^2n^2}.$$
This proves that
$$S_2=\frac{1}{2}\sum_{m\in\Bbb{N}_1}\frac{1}{m^2}\sum_{n\in\Bbb{N}_1}\frac{1}{n^2}=\frac{1}{2}\big(\zeta(2)\big)\big(\zeta(2)\big)=\frac{1}{2}\left(\frac{\pi^2}{6}\right)^2=\frac{\pi^4}{72}.$$
Now, for $S_1$, we see that the last term is
$$\sum_{n=1}^\infty\frac{1}{8n^4}=\frac{1}{8}\zeta(4)=\frac{1}{8}\left(\frac{\pi^4}{90}\right)=\frac{\pi^4}{720}.$$
We are left with the first term, which is
$$\sum_{m,n\in\Bbb{N}_1}\frac{1}{2mn(m+n)^2}=\zeta(3,1)=\frac{1}{4}\zeta(4)=\frac{1}{4}\left(\frac{\pi^4}{90}\right)=\frac{\pi^4}{360},$$
by Robert Z's answer. Thus,
$$S_1=\frac{\pi^4}{360}-\frac{\pi^4}{720}=\frac{\pi^4}{720}.$$
Combining the two results above, we have
$$S=S_1+S_2=\frac{\pi^4}{720}+\frac{\pi^4}{72}=\frac{11\pi^4}{720}=\frac{11}{8}\zeta(4).$$
Here is another great resource to learn about the multiple zeta function. Corollary 1.64 on page 26 and discussions that lead to this corollary are important to this problem.
Here is an elementary way to show that $\zeta(3,1)=\frac{1}{4}\zeta(4)$. Recall that
$$\zeta(s_1,s_2,\ldots,s_t)=\sum_{\substack{{n_1,n_2,\ldots,n_t\in\Bbb{N}_1} \\{n_1>n_2>\ldots>n_t}}} \frac{1}{n_1^{s_1}n_2^{s_2}\cdots n_t^{s_t}}.$$
First, observe that
$$\frac{1}{m^2n^2}=\frac{1}{(m+n)^2n^2}+\frac{1}{(m+n)^2m^2}+\frac{2}{(m+n)^3m}+\frac{2}{(m+n)^3n}.$$
Taking the sum of the expression above over $m,n\in\Bbb{N}_1$, we get
$$\big(\zeta(2)\big)^2=\zeta(2,2)+\zeta(2,2)+2\zeta(3,1)+2\zeta(3,1)=2\big(\zeta(2,2)+2\zeta(3,1)\big),\tag{1}$$
so
$$\zeta(2,2)+2\zeta(3,1)=\frac{1}{2}\big(\zeta(2)\big)^2=\frac{5}{4}\zeta(4).$$
Now, note that
$$\frac{5}{2}\zeta(4)=\big(\zeta(2)\big)^2=\sum_{m,n\in\Bbb{N}_1}\frac{1}{m^2n^2}=\sum_{n\in\Bbb{N}_1}\frac{1}{n^4}+\sum_{\substack{{m,n\in\Bbb{N}_1}\\{m>n}}}\frac{1}{m^2n^2}+\sum_{\substack{{m,n\in\Bbb{N}_1}\\{m<n}}}\frac{1}{m^2n^2}.$$
Hence,
$$\frac{5}{2}\zeta(4)=\zeta(4)+\zeta(2,2)+\zeta(2,2),$$
making
$$\zeta(2,2)=\frac{3}{4}\zeta(4).\tag{2}$$
Combining (1) and (2), we obtain
$$\zeta(3,1)=\frac{1}{2}\left(\frac{5}{4}\zeta(4)-\zeta(2,2)\right)=\frac{1}{4}\zeta(4).$$