Here is a possible explanation for what you have observed. In your first equation the Berry phase is, as you say,
$$
\gamma_n(t) = i\int_0^t dt' \, \langle n(t') |\dot{n}(t')\rangle.
$$
However the term $e^{i\gamma_n}$ (as well as the other, dynamical phase) is simply a phase and so it is un-important in quantum mechanics and can safely be discarded.
It can also be discarded in the following sense. The eigenvector $|n(t)\rangle$ is only defined up to a phase. I could redefine $|n(t)\rangle$ for each $t$ in such a way as to absorb the Berry phase (and the dynamical phase too).
However now imagine the following situation. Your system (or if you want your Hamiltonian) depends on some number $n$ of real parameters $X_1,\ldots, X_n$. You can imagine to change these parameters very slowly, i.e. adiabatically, along a certain path $\mathbf{r}(t)=(X_1(t),\ldots, X_n(t)$ with $t\in[0,\tau]$.
Now imagine that the path is closed, that is $\mathbf{r}(0)=\mathbf{r}(\tau)$. In other words you traveled somewhere (very slowly) in parameter space and came back to the initial point. In this case you can quickly see that the Berry phase becomes a geometrical object:
\begin{align}
\gamma_n(t) &= i\int_0^\tau dt' \, \langle n(t') |\dot{n}(t')\rangle \\
&= i\oint dX\, \langle n(r) |\nabla_X {n}(r)\rangle
\end{align}
It also turns out that this term can no longer be reabsorbed by a continuous reparametrization of the eigenstate $|n(t)\rangle$. In some situations it is even possible to observe this term.
Sometimes it is this specific term that is called Berry phase.
In short:
The Berry phase does not disappear when including the first order corrections. Simply for an open adiabatic path the Berry phase can be discarded and this is probably what was intended in the paper you linked. For a cyclic adiabatic transformation the Berry phase becomes a geometrical object and can even be observed.