It turns out rewriting the function in terms of Bernouilli numbers etc, while useful in generating specific values of $F(m,N)$, is not an easy path to proving they are integers. The following proof is reasonably elementary (knowledge of complex $n$th roots of $1$, no calculus) and is drawn from D. Zagier, Elementary Aspects of the Verlinde Formula and of the Harder-Narasimhan-Atiyah-Bott Formula, Israel Math. Conf. Proc. 9 (1996) - see Theorem 1 part (vii). (I've given more detail on some of the steps, and structured it to focus on the proof of integral value).
PS - I'm an actuary, with no academic credentials beyond a Maths BA from 30 years ago, but I've enjoyed reading your comments and finding a solution to a tweet that I read 1 year ago (almost to the day!) and which has bugged me ever since.
APPROACH
Fix N.
(1) We will define a function $f(g,\mathbf{x})$ on integer $g \geq 0$ and $\mathbf{x}=(x_1,x_2,...,x_{N-1})$ for integer $x_i \geq 0$.
Then, defining $\mathbf{e_1}=(1,0,0,...0), \mathbf{e_2}=(0,1,0,...,0), ... \mathbf{e_{N-1}}=(0,0,...0,1)$
we will show
(2) $f(m+1,\mathbf{0}) = F(m,N)$
(3) $f(0,\mathbf{0})$ is an integer
(4) $f(0,\mathbf{e_t})$ is an integer
(5) $f(0,\mathbf{e_t+e_u})$ is an integer
(6) $f(0,\mathbf{e_t+e_u+e_v})$ is an integer
(7) $\displaystyle \sum_{t} f(0,\mathbf{x+e_t})f(0,\mathbf{y+e_t})=f(0,\mathbf{x+y})$ for all $\mathbf{x,y}$
(8) using (3) - (7), $f(0,\mathbf{x})$ is an integer for all $\mathbf{x}$
(9) $\displaystyle \sum_{t} f(g,\mathbf{x+2e_t})= f(g+1,\mathbf{x})$ for all $g$
(10) using (8) - (9), $f(g,\mathbf{x})$ is an integer for all $g$ and $\mathbf{x}$
and so conclude from (2) and (10) that $F(m,N)$ is an integer.
All summations are over $\{1,2,...,N-1\}$.
STEPS (1), (2)
(1)
Let
$s(z)=\displaystyle \frac{-2N}{(z - z^{-1})^2}$
$r_a(z) =\displaystyle \frac{z^{a} - z^{-a}}{z - z^{-1}}$
$r(z,\mathbf{x}) = \displaystyle\prod_a r_a(z)^{x_a}$
$\omega = e^{i \pi / N}$
$f(g,\mathbf{x})=\displaystyle \sum_{j=1}^{N-1} s(\omega^j)^{g-1}r(\omega^j,\mathbf{x})$
(2)
$s(\omega^j) = \displaystyle\frac{-2N}{(2i\sin(\pi j / N))^2}=\frac{N}{2\sin^2(\pi j / N)}\quad$ and $\quad r(\omega^j,\mathbf{0})=1\quad$ so
$f(m+1,\mathbf{0})=(\frac{N}{2})^m\sum\frac{1}{\sin^{2m}(\pi j/N)} = F(m,N)$
USEFUL RESULTS
For the next steps, the following will be useful.
Let $T_k=\displaystyle \sum_j \omega^{jk} + \omega^{-jk}$ and $U_k=\displaystyle\sum_j \frac{\omega^{jk}-\omega^{-jk}}{\omega^j-\omega^{-j}}$
Then (derivation in footnote):
$\begin{cases}
T_k = 2(N-1), & U_k = 0 & \text{if $k$ is multiple of $2N$} \\
T_k = -2, & U_k = 0 & \text{if $k$ even, and not a multiple of $2N$}\\
T_k = 0, & U_k = N-k+2Nq & \text{if $k$ odd (some integer $q$)}\\
\end{cases}$
STEPS (3) - (6)
(3)
$f(0,\mathbf{0}) = \displaystyle \sum_j \frac{(\omega^j - \omega^{-j})^2}{-2N}=\frac{-1}{2N}\sum (\omega^{2j}+\omega^{-2j}-2)=\frac{-1}{2N}(T_2 - 2(N-1)) = 1$
(4)
$r(\omega^j, \mathbf{e_t})= \displaystyle \frac{\omega^{jt} - \omega^{-jt}}{\omega^j - \omega^{-j}}$,
so $r(\omega^j,\mathbf{e_1})=1$, so $f(0,\mathbf{e_1})=1$
For $t>1$,
$f(0,\mathbf{e_t})=\displaystyle -\frac{1}{2N} \sum_j (\omega^j-\omega^{-j})(\omega^{jt} - \omega^{-jt})=-\frac{1}{2N}(T_{t+1}-T_{t-1})=0$
(5)
$r(\omega^j,\mathbf{e_t+e_u})=\displaystyle \frac{\omega^{jt} - \omega^{-jt}}{\omega^j - \omega^{-j}}\frac{\omega^{ju} - \omega^{-ju}}{\omega^j - \omega^{-j}}$ so
$f(0,\mathbf{e_t+e_u})=-\displaystyle\frac{1}{2N}\sum_j (\omega^{j(t+u)}+\omega^{-j(t+u)}-\omega^{j(u-t)}-\omega^{-j(u-t)})$
$=-\frac{1}{2N}(T_{t+u}-T_{t-u})$ from which
$f(0,\mathbf{e_t+e_u})=
\begin{cases}
1 & \text{if }t = u \\
0 & \text{if }t \neq u
\end{cases}$
(6)
$f(0,\mathbf{e_t+e_u+e_v})=\displaystyle -\frac{1}{2N}\sum_j\frac{(\omega^{jt} - \omega^{-jt})(\omega^{ju} - \omega^{-ju})(\omega^{jv} - \omega^{-jv})}{\omega^j - \omega^{-j}}$
$=-\frac{1}{2N}(U_{t+u+v}-U_{t+u-v}+U_{t-u-v}-U_{t-u+v})$
If $t+u+v$ etc are even, then this is $0$.
If $t+u+v$ etc are odd, then (since $U_k = N - k + \text{multiple of $2N$}$)
$U_{t+u+v}-U_{t+u-v}+U_{t-u-v}-U_{t-u+v}$
$=(t+u+v)-(t+u-v)+(t-u-v)-(t-u+v)+2Nq = 2Nq$ for integer $q$.
So $f(0,\mathbf{e_t+e_u+e_v})$ is an integer.
ANOTHER USEFUL RESULT
Let $a_{jk} =\displaystyle \sum_t r_t(\omega^j)r_t(\omega^k)=\frac{\sum (\omega^{jt} - \omega^{-jt})(\omega^{kt}-\omega^{-kt})}{(\omega^j-\omega^{-j})(\omega^k-\omega^{-k})}$
Along similar lines to (4), this is $0$ except
$a_{jj}=\displaystyle \frac{1}{(\omega^j - \omega^{-j})^2}(T_{2j}-2(N-1))=\frac{-2N}{(\omega^j - \omega^{-j})^2}$
So $a_{jk}=
\begin{cases}
s(\omega^j) & \text{if }j=k\\
0 & \text{otherwise}
\end{cases}$
STEPS (7) - (10)
(7)
$\displaystyle \sum_{t} f(0,\mathbf{x+e_t})f(0,\mathbf{y+e_t})$
$=\displaystyle \sum_t \left[ \sum_j s(\omega^j)^{-1}\prod_a r_a(\omega^j)^{x_a}\cdot r_t(\omega^j) \sum_k s(\omega^k)^{-1}\prod_b r_b(\omega^k)^{y_b}\cdot r_t(\omega^k) \right]$
$=\displaystyle \sum_j \sum_k s(\omega^j)^{-1}s(\omega^k)^{-1}\prod_a r_a(\omega^j)^{x_a}\prod_b r_b(\omega^k)^{y_b}\sum_t r_t(\omega^j) r_t(\omega^k)$
$=\displaystyle\sum_j s(\omega^j)^{-1} s(\omega^j)^{-1}\prod_a r_a(\omega^j)^{x_a+y_b}s(\omega^j)$ using the previous result for $a_{jk}$
$=f(0,\mathbf{x+y})$
(8)
Let $A_n = \{\mathbf{x}:x_i \geq 0, x_1+x_2+...+x_{N-1} = n\}$
We prove by induction on $n$, that $f(0,\mathbf{x})$ is an integer for $\mathbf{x} \in A_n$
The results from (3) - (6) show this is the case for $n \leq 3$.
So pick $n \geq 4$ and assume that the function is an integer for $A_m$ for all $m < n$.
$\mathbf{x} \in A_n \implies$ for some $a$ and $b$, $\mathbf{x-e_a-e_b} \in A_{n-2}$
so applying (7), $\displaystyle \sum_t f(0,\mathbf{x-e_a-e_b+e_t})f(0,\mathbf{e_a+e_b+e_t})=f(0,\mathbf{x})$
So $f(0,\mathbf{x})$ is an integer, because $\mathbf{x-e_a-e_b+e_t} \in A_{n-1}$ and $\mathbf{e_a+e_b+e_t} \in A_3$ so these give integer values by induction assumption.
(9)
$\displaystyle \sum_{t} f(g,\mathbf{x+2e_t})=\sum_t \sum_j s(\omega^j)^{g-1}r(\omega^j,\mathbf{x})r_t(\omega^j)^2$
$=\displaystyle \sum_j s(\omega^j)^{g-1}r(\omega^j,\mathbf{x})\sum_t r_t(\omega^j)r_t(\omega^j) = \sum_j s(\omega^j)^gr(\omega^j,\mathbf{x})$ using the $a_{jj}$ result
so $\displaystyle \sum_{t} f(g,\mathbf{x+2e_t})=f(g+1,\mathbf{x})$
(10)
It is a straightforward induction on $g$ using (8) and (9), to deduce that $f(g,\mathbf{x})$ is an integer for all $g$.
This completes the proof.
FOOTNOTE
Note that $\omega^{Nk} = (-1)^k$ and $\omega^{-1} = \omega^{2N-1}$
If $k$ is a multiple of $2N$ then $\omega^k = \omega^{-k}=1$, so $T_k = 2(N-1)$, $U_k=0$
Otherwise, summing as geometric progressions,
$T_k= \displaystyle \frac{\omega^k-\omega^{Nk}+\omega^{(N+1)k}-1}{1-\omega^k}$ which simplifies to
$-2$ if $k$ is even and $0$ if $k$ is odd.
It is straightforward to show that
$\displaystyle\frac{\omega^{jk}-\omega^{-jk}}{\omega^j-\omega^{-j}}=\omega^{j(k-1)}+\omega^{-j(k-1)}+\omega^{j(k-3)}+\omega^{-j(k-3)}+...+\omega^{jp}+\omega^{-jp}+a$
where
$p = 2$ and $a=1$ if $k$ is odd,
$p=1$ and $a=0$ if $k$ is even.
Thus $U_k=T_{k-1} + T_{k-3} + ... T_p+(N-1)a$
If $k$ is even then $U_k=0$
If $k$ is odd, then $T_{k-1} + ... + T_p$ contains $(k-1)/2$ instances of $T_{\text{even}}$ which are either $-2$ or $-2+2N$, so $U_k = -(k-1) + 2Nq + (N-1)$ where $q$ counts the occurrences of multiples of $2N$ in $\{2, 4, ... k-1\}$.
So, if $k$ is odd, $U_k = N-k+2Nq$ for some integer $q$.