I realize it's been a while, but I thought this one looked interesting, so I thought I would give it a go.
Make the obvious sub $\displaystyle t=\frac{-\ln(x)}{2\pi}, \;\ x=e^{-2\pi x}, \;\ dx=-2\pi e^{-2\pi x}dx$
$\displaystyle2\pi\int_{0}^{\infty}\ln(t^{2}+1)\ln(1-e^{-2\pi t})dt$.
Use parts $\displaystyle u=\ln(1-e^{-2\pi t}), \;\ dv=\ln(t^{2}+1)dt, \;\ v=x\ln(t^{2}+1)+2(\tan^{-1}(t)-t), \;\ du=\frac{2\pi}{e^{2\pi t}-1}dt$
$\displaystyle -2\pi \left(2\pi\int_{0}^{\infty}\left(t\ln(t^{2}+1)+2\tan^{-1}(t)-2t\right)\cdot \frac{1}{e^{2\pi t}-1}\right)dt$
$=\displaystyle -4\pi^{2} \left(\int_{0}^{\infty}\frac{t\ln(t^{2}+1)}{e^{2\pi t}-1}dt+2\int_{0}^{\infty}\frac{\tan^{-1}(t)}{e^{2\pi t}-1}dt-2\int_{0}^{\infty}\frac{t}{e^{2\pi t}-1}dt\right)$
Now, the two leftmost integrals form a rather well-known identity that can be derived from Hermite's integral (among other ways).
$\displaystyle\int_{0}^{\infty}\frac{t\ln(t^{2}+1)}{e^{2\pi t}-1}dt+2\int_{0}^{\infty}\frac{\tan^{-1}(t)}{e^{2\pi t}-1}dt=\zeta'(-1)+1/4$
The integral on the right end is rather elementary and evaluates to $\displaystyle 2\int_{0}^{\infty}\frac{t}{e^{2\pi t}-1}dt=1/12$
Putting the pieces together results in $\displaystyle-4\pi^{2}\left(\zeta'(-1)+1/4-1/12\right)=-4\pi^{2}\zeta'(-1)-\frac{2\pi^{2}}{3}$
Hermite's integral
$\displaystyle\zeta (a,t)=\sum_{n=0}^{\infty}\frac{1}{(n+t)^{a}}=\frac{t^{-a}}{2}+\frac{t^{1-a}}{a-1}+i\int_{0}^{\infty}\frac{(t+ix)^{-a}-(t-ix)^{-a}}{e^{2\pi x}-1}dx$
Diffing this w.r.t a leads to
$\displaystyle \zeta'(a,t)=\frac{-t^{-a}}{2}log(t)-\frac{t^{1-a}(1+(a-1)log(t))}{(a-1)^{2}}+i\int_{0}^{\infty}\frac{(t-ix)^{-a}log(t-ix)-(t+ix)^{-a}log(t+ix)}{e^{2\pi x}-1}dx$
By letting $a=-1, \;\ t=1$ leads to the two log/arctan integrals in question.