$$\begin{eqnarray*}\sum_{n\geq 1}\frac{x^n}{n^2 \binom{2n}{n}}&=&\sum_{n\geq 1}\frac{(n-1)!^2}{(2n)!} x^n = \sum_{n\geq 1}B(n,n)\frac{x^n}{2n}=\int_{0}^{1}\sum_{n\geq 1}y^{n-1}(1-y)^{n-1}\frac{x^n}{2n}\\&=&-\frac{1}{2}\int_{0}^{1}\frac{\log(1-xy+xy^2)}{y(1-y)}\,dy\end{eqnarray*} $$
hence by taking $\sigma_+=\frac{3+\sqrt{5}}{2}$ and $\sigma_-=\frac{3-\sqrt{5}}{2}$:
$$\begin{eqnarray*}\sum_{n\geq 1}\frac{F_{2n}}{n^2\binom{2n}{n}}&=&-\frac{1}{2\sqrt{5}}\int_{0}^{1}\frac{\log(1-\sigma_{+}(y-y^2))-\log(1-\sigma_{-}(y-y^2))}{y(1-y)}\,dy\\&=&-\frac{2}{\sqrt{5}}\int_{0}^{1}\frac{\log(1-\sigma_+(1-u^2)/4)-\log(1-\sigma_-(1-u^2)/4)}{1-u^2}\,du\end{eqnarray*}$$
and the last integral can be computed by exploiting the well-known relations between the dilogarithm and the golden ratio. Another technique is shown in one of the answers I am most proud of, a cooperative work by me, achille hui and Bhenni Benghorbal. It gives that the problem boils down to computing a squared arcsine.