If we consider the dihedral group of order 12, $G = \langle a, b \mid a^2 = b^2 = (ab)^6 = e \rangle$, then the Cayley graph corresponding to $\{ a, b \}$ is the cyclic graph on 12 vertices with edges labeled alternately by $a$ and $b$. We may then consider $H_1 = G \times \mathbb Z/2 \mathbb Z$ and $H_2 = G \rtimes \mathbb Z/2 \mathbb Z$ where the copies of $\mathbb Z/ 2 \mathbb Z$ are generated by $c$ and $d$ respectively, and where $d$ acts by $d a d = b$, $d b d = a$. Then the Cayley graph of $H_1$ with respect to $\{ a, b, c \}$ consists of two copies of cyclic graphs of order 12 with edges labeled by $c$ connecting the two graphs. Since $d$ just interchanges $a$ and $b$ we have that the Cayley graph of $H_2$ with respect to $\{ a, b, d \}$ can be obtained from the Cayley graph of $H_1$ by just relabeling the second copy of the cyclic graph, so that the two Cayley graphs will be isomorphic.
Unfortunately, the generating set for $H_2$ is not minimal since by the definition of $d$ we have $b \in \langle a, d \rangle$. This can be fixed however by taking two automorphisms $c$ and $d$ which are complicated enough so that this doesn't occur.
Specifically, we can let $c$ act on $G$ by $cac = ababa$, and $cbc = babab$, and we can let $d$ act on $G$ by applying $c$ and then interchanging $a$ and $b$, i.e., $dad = babab$, and $dbd = ababa$. It's not hard to see that these indeed define order two automorphisms of $G$, and for the same reason as above we have that the Cayley graphs of $H_1$ and $H_2$ will be isomorphic.
It is also not hard to check that we now have $| \langle a, c \rangle | = | \langle b, c \rangle | = 12 < 24$ and $| \langle a, d \rangle | = | \langle a, d \rangle | = 8 < 24$ so that the generating sets are now minimal. Moreover, the groups $H_1$ and $H_2$ will not be isomorphic, this can be seen for instance by counting the number of elements of order 2, (I counted 15 for $H_1$ and 9 for $H_2$, but I've omitted the tedious details).