[guided]The main issue is not bijectivity on each fiber; the frame already gives that. The point is to prove that the fiber coordinates vary smoothly with the base point. We do this by translating the statement into an ordinary matrix calculation in a local bundle chart.
Choose an open set $V \subset U$ on which the vector bundle is trivial, and choose a smooth local bundle chart $\theta: E|_V \to V \times \mathbb{R}^r$. This chart is fiberwise linear: for each $x \in V$, the restricted map $\theta|_{E_x}: E_x \to \{x\} \times \mathbb{R}^r$ is a linear isomorphism after identifying $\{x\} \times \mathbb{R}^r$ with $\mathbb{R}^r$.
Each frame section $s_i: U \to E|_U$ restricts to a smooth section over $V$. Because $\theta(s_i(x))$ lies over $x$, there is a unique vector $b_i(x) \in \mathbb{R}^r$ such that
\begin{align*}
\theta(s_i(x)) = (x,b_i(x)).
\end{align*}
This defines a map $b_i: V \to \mathbb{R}^r$. The map $b_i$ is smooth because it is obtained by composing the smooth section $s_i$, the smooth chart $\theta$, and the smooth projection map $\operatorname{pr}_2:V\times\mathbb{R}^r\to\mathbb{R}^r$, $\operatorname{pr}_2(x,v)=v$.
Now assemble these coordinate vectors into a matrix. Define $A: V \to \operatorname{Mat}_{r \times r}(\mathbb{R})$ by taking the $i$th column of $A(x)$ to be $b_i(x)$. Since each entry of each $b_i$ is smooth, each entry of $A$ is smooth. For a fixed $x \in V$, the vectors $(s_1(x),\dots,s_r(x))$ are a basis of $E_x$. Applying the linear isomorphism $\theta|_{E_x}$ sends this basis to $(b_1(x),\dots,b_r(x))$, so these vectors form a basis of $\mathbb{R}^r$. Thus $A(x)$ is invertible, equivalently $\det A(x) \neq 0$, for every $x \in V$.
In the chart $\theta$, the map $\Psi$ has the concrete form
\begin{align*}
(\theta \circ \Psi)(x,a) = (x,A(x)a).
\end{align*}
Indeed, if $a=(a_1,\dots,a_r)$, then fiberwise linearity of $\theta$ gives
\begin{align*}
\theta\left(\sum_{i=1}^r a_i s_i(x)\right) = \left(x,\sum_{i=1}^r a_i b_i(x)\right) = (x,A(x)a).
\end{align*}
The coordinate functions of $(x,a) \mapsto (x,A(x)a)$ are finite sums of products of smooth functions, so this map is smooth. Hence $\Psi$ is smooth on $V \times \mathbb{R}^r$. Since the trivialising sets $V$ cover $U$, smoothness holds globally.
For the inverse, take $e \in E|_V$ and write $\theta(e)=(x,v)$ with $x \in V$ and $v \in \mathbb{R}^r$. The unique coefficients $a \in \mathbb{R}^r$ satisfying
\begin{align*}
e = \sum_{i=1}^r a_i s_i(x)
\end{align*}
are exactly the solution of the linear system $A(x)a=v$. Since $A(x)$ is invertible, this solution is $a=A(x)^{-1}v$, so
\begin{align*}
\Psi^{-1}(e) = (x,A(x)^{-1}v).
\end{align*}
The inverse matrix depends smoothly on $x$: by the adjugate formula,
\begin{align*}
A(x)^{-1} = \frac{1}{\det A(x)}\operatorname{adj}(A(x)).
\end{align*}
The adjugate entries are polynomial expressions in the entries of $A(x)$, and division by $\det A(x)$ is smooth because $\det A(x)$ is nowhere zero on $V$. Therefore $(x,v) \mapsto (x,A(x)^{-1}v)$ is smooth. This proves that $\Psi^{-1}$ is smooth locally in every bundle chart, and hence smooth globally.[/guided]