First I want to amplify on a comment of @Phillip Hamilton, which I think gives the most mathematically precise take on the problem. (It is not necessary to be so precise and some may think it is overly fastidious to do so for the intended application...but this is what the OP asked about, I think.)
For an alphabet $\Sigma$ and a positive integer $k$, let $S(\Sigma,k)$ be the set of strings of length $k$ in the alphabet $\Sigma$. For $x,y \in S(\Sigma,k)$,
we are defining an equivalence relation $x \sim y$, called y is a shuffle of x, that is defined in terms of getting from $x$ to $y$ by applying some permutation $\pi \in S_k$. So "Is a shuffle the same as a permutation?" No,
because if the strings are e.g.
$x = aaabaaa$
and
$y= aabaaaa$
there is a permutation $\pi$ that takes one to the other, but there is more than one such permutation $\pi$.
This can be most precisely understood in the language of group actions. There is a natural -- permutation! -- action of the symmetric group $S_k$ on $S(\Sigma,k)$. Whenever a group $G$ acts on a set $X$, it determines a partition of the set into orbits under the group: that is, for $x \in X$,
the orbit is $\{ g \cdot x \mid g \in G\}$. The corresponding equivalence relation is $x \sim y$ if $y = g \cdot x$ for some $g \in X$. Taking here
$G = S_k$ and $X = S(\Sigma,k)$ we get exactly the definition of "$y$ is a shuffle of $x$."
Now suppose $x$ and $y$ are in the same orbit of $G$: thus there is $g_0 \in G$
such that $g_0 \cdot x = y$. If we put $H_x = \{h \in x \mid h \cdot x = x\}$,
the stabilizer of $x$ in $G$, then
$\{g \in G \mid g \cdot x = y\} = g_0 H_x$,
i.e., it is a coset of the stabilizer.
So in the present case, there is more than one permutation inducing the same shuffle from $x$ to $y$ precisely when there is a nontrivial permutation $\pi$
such that $\pi \cdot x= x$. In the example above, there are many such permutations: in the example I gave above, the stabilizer of $x$ is a copy of $S_6$: you can freely permute all the $a$'s.
Second: I think the above is helpful in clarifying that to determine whether $y$ is a shuffle of $x$ one need not apply all permutations to $x$ to see if one gets $y$ (which would take time at least $k!$). Indeed $y$ is a shuffle of $x$ precisely when each "letter" in $\Sigma$ appears the same number of times in $x$ as it does in $y$.
There is an obvious algorithm for this: count the number of times the letter $x_1$ appears in $y$. If they are different, $y$ is not a shuffle of $x$. Now move on to $x_2$, and so forth. There are some obvious ways to speed this up (e.g. by recording when a letter appears in $x$ and not counting instances of the same letter more than once!), but this is already of time $O(k^2)$.