Let $H_q$ denote harmonic numbers (generalized to a non-integer index $q$): $$H_q=\sum_{k=1}^\infty\left(\frac1k-\frac1{k+q}\right)=\int_0^1\frac{1-x^q}{1-x}dx=\gamma+\psi(q+1),\tag1$$ where $\psi(z)=\Gamma'(z)/\Gamma(z)$ is the digamma function.
My goal is to evaluate the following series: $$\mathcal S_m=\sum_{n=1}^\infty\frac{(-1)^n\,H_{n/m}}n.\tag2$$ Using the integral representation from $(1)$ we can get equivalent integral forms: $$\mathcal S_m=\int_0^1\frac{\ln(1+\sqrt[m]x)-\ln2}{1-x}\,dx=m\int_0^1\frac{\ln(1+z)-\ln2}{1-z^m}\,z^{m-1}dz.\tag3$$ Here are some simple cases: $$\begin{align}&\mathcal S_1=\frac{\ln^22}2-\frac{\pi^2}{12}\hspace{7.7em}\color{maroon}{\mathcal S_2=\ln^22-\frac{\pi^2}{12}}\\\\&\color{blue}{\mathcal S_3=\frac{3\ln^22}2-\frac{\pi^2}9+\frac12\,\operatorname{Li}_2\!\left(\tfrac14\right)}\hspace{2em}\color{green}{\mathcal S_4=\frac{7\ln^22}4-\frac{5\pi^2}{48}}\end{align}\tag4$$ For $\mathcal S_5$ the integral can be found using Mathematica (there is even a closed-form antiderivative, so it should be possible in principle to prove it by differentiation), but the result takes tens of thousands characters to write down (you can see it here), and Mathematica cannot do much simplification on it (here is a simplified result).
But I was able to conjecture a much simpler closed form that fits numerically with a high precision:
$$\mathcal S_5\stackrel{\color{gray}?}=\frac{\ln^22}2-\frac{\ln^25}4+\ln2\cdot\ln5-\frac12\,\operatorname{Li}_2\!\left(\tfrac15\right)-\operatorname{Li}_2\!\left(\frac{\sqrt5-1}2\right)\tag{$\diamond$}$$
I hope there is a way to prove this result manually without going through huge intermediate expressions, but so far I have not found it.
Here is how one can compute $\mathcal S_m$ for arbitrary $m$.
Your formula (3) can be rewritten as $$\mathcal{S}_m=-m\int_0^1\frac{\ln\frac{1+z}{2}}{z^m-1}z^{m-1}dz=-m\sum_{k=0}^{m-1}\alpha_{km}\int_0^1\frac{\ln\frac{1+z}{2}}{z-e^{2\pi i k/m}}dz,$$ where $$\alpha_{km}=\lim_{\quad z\to\; \exp{\frac{2\pi i k}m}}\frac{z^{m-1}\left(z-e^{2\pi i k/m}\right)}{z^m-1}=\frac{e^{2\pi i k(m-1)/m}}{\prod_{n\ne k}\left(e^{2\pi i k/m}-e^{2\pi i n/m}\right)}=\frac1m.$$ Note in particular that the last expression is independent of $k$.
The remaining integrals can be computed in terms of polylogarithms: $$I\left(\zeta\right)=\int_0^1\frac{\ln\frac{1+z}{2}}{z-\zeta}dz= \operatorname{Li}_2\left(\frac{2}{1+\zeta}\right)- \operatorname{Li}_2\left(\frac{1}{1+\zeta}\right)+ \ln2\ln\frac{\zeta}{1+\zeta}.\tag{1}$$ We have in particular $$I\left(1\right)=\frac{\pi^2}{12}-\frac{\ln^22}{2},\qquad I\left(-1\right)=-\frac{\ln^22}{2}. $$
This implies that $$\mathcal{S}_m=-\sum_{k=0}^{m-1}I\left(e^{2\pi i k/m}\right), \tag{2}$$ with $I\left(\zeta\right)$ defined by (1). It is clear that under the sum the elementary pieces of $I(\zeta)$ simplify. It might happen that something nice happens also with the dilogarithmic ones.
Update 1 (how to simplify one of the two sums of dilogarithms to an elementary expression):
We also have the identity $\operatorname{Li}_2\left(z\right)=-\operatorname{Li}_2\left(\frac{z}{z-1}\right)-\frac12\ln^2\left(1-z\right)$, which can be rewritten as $$\operatorname{Li}_2\left(\frac{1}{\zeta+1}\right)=-\operatorname{Li}_2\left(-\zeta^{-1}\right)-\frac12\ln^2\frac{\zeta}{\zeta+1}.$$
Combining both results, we obtain for odd $m$ $$\sum_{k=0}^{m-1}\operatorname{Li}_2\left(\frac{1}{1+e^{2\pi i k/m}}\right)= \frac{\pi^2}{12m}-\frac12\sum_{k=0}^{m-1}\ln^2\left(1+e^{-2\pi i k /m}\right),$$ and for even $m$ $$\sum_{k=0 | k\neq \frac{m}{2}}^{m-1}\operatorname{Li}_2\left(\frac{1}{1+e^{2\pi i k/m}}\right)= \frac{\pi^2(m-1)}{6m}-\frac12\sum_{k=0| k\neq \frac{m}{2}}^{m-1}\ln^2\left(1+e^{-2\pi i k /m}\right).$$
Update 2 (simplification of the remaining sum for even $m$):
We can use again the identity $\operatorname{Li}_2\left(z\right)=-\operatorname{Li}_2\left(\frac{z}{z-1}\right)-\frac12\ln^2\left(1-z\right)$ to show that $$\operatorname{Li}_2\left(\frac{2}{1+\zeta}\right)+\operatorname{Li}_2\left(\frac{2}{1-\zeta}\right)=-\frac12\ln^2\frac{\zeta-1}{\zeta+1}.$$ For even $m$, if $\zeta$ is an $m$th root of unity, then so is $-\zeta$, which simplifies the second sum to an elementary expression: $$\sum_{k=0 | k\neq \frac{m}{2}}^{m-1}\operatorname{Li}_2\left(\frac{2}{1+e^{2\pi i k/m}}\right)=\frac{\pi^2}{12}-\frac{\ln^2 2}{2}-\frac12\sum_{k=1}^{\frac{m}{2}-1}\ln^2\frac{e^{2\pi i k/m}-1}{e^{2\pi i k/m}+1}.$$ Altogether, this leads to evaluation \begin{align*} \mathcal{S}_{2n}&=\frac{\ln 2\ln 8n^2}{2}-\frac{\pi^2}{12n}+\frac12 \sum_{k=1}^{n-1}\ln^2\frac{e^{\pi i k/n}-1}{e^{\pi i k/n}+1}-\frac12\sum_{k=0| k\neq n}^{2n-1}\ln^2\left(1+e^{-\pi i k /n}\right)=\\ &=\ln 2\ln 2n-\frac{\pi^2\left(n^2+1\right)}{24n}-\sum_{k=1}^{n-1}\ln\left(2\sin\frac{\pi k}{2n}\right)\ln\left(2\cos\frac{\pi k}{2n}\right). \tag{$\spadesuit$} \end{align*}
Update 3 (partial simplification for odd $m$)
Let us denote $m=2n+1$. We will use the identity $$\operatorname{Li}_2\left(\frac{2}{1+\zeta}\right)=\operatorname{Li}_2\left(\frac{\zeta+1}{\zeta-1}\right)+\frac12 \ln^2 \frac{\zeta-1}{\zeta+1} -\ln\left(-\frac{2}{1+\zeta}\right)\ln\frac{\zeta-1}{\zeta+1}-\frac{\pi^2}{6}. \tag{3}$$ Now the key three facts are that
If $\zeta$ is $\zeta^m=1$, then so is $\zeta^{-1}$.
Under replacement $\zeta\leftrightarrow \zeta^{-1}$, the dilogarithm argument on the right of (3) changes its sign.
There is an identity $\operatorname{Li}_2\left( z\right)+ \operatorname{Li}_2\left( - z\right)=\frac{1}{2}\operatorname{Li}_2\left( z^2\right)$.
Put altogether, this leads to \begin{align*}\sum_{k=0}^{m-1}\operatorname{Li}_2\left(\frac{2}{1+e^{\frac{2\pi i k}{m}}}\right)=&\frac12\sum_{k=1}^n\operatorname{Li}_2\left(-\cot^2\frac{\pi k}{2n+1}\right)+\frac{4n^2+3n+2}{2n+1}\cdot\frac{\pi^2}{12}+\\ &+\sum_{k=1}^n\ln\left(\tan\frac{\pi k}{2n+1}\right) \ln\left(\frac12\sin\frac{2\pi k}{2n+1}\right). \end{align*} Combining this with the previous results of Update 1, we finally arrive at \begin{align} \nonumber\mathcal{S}_{2n+1}=& -\frac12\sum_{k=1}^n\operatorname{Li}_2\left(-\cot^2\frac{\pi k}{2n+1}\right)-\sum_{k=1}^n\ln^2\sin\frac{\pi k}{2n+1} +\\ &+\left(n+\frac12\right)\ln^2 2-\frac{\left(2n^2+n+1\right)\pi^2}{12\left(2n+1\right)}.\tag{$\clubsuit$} \end{align} Remark. For $n=2$ (i.e. $m=5$) this sum contains two dilogarithms $\operatorname{Li}_2\left(-1\pm\frac{2}{\sqrt5}\right)$. One should be able to reduce them to just one $\operatorname{Li}_2\left(\frac15\right)$ using a suitable identity.