Here’s another approach. Name the boxes $a$, $b$, $c$, and $d$. If $S\subseteq\{a,b,c,d\}$, define $e_S$ to be the probability that each box whose name is an element of $S$ is empty after all four balls have been placed. (Boxes not named in $S$ might also be empty.)
Then, using the inclusion-exclusion principle, the probability $p_{\{a\}}$ that only box $a$ is empty is
$p_{\{a\}}=e_{\{a\}}-e_{\{a,b\}}-e_{\{a,c\}}-e_{\{a,d\}}+e_{\{a,b,c\}}+e_{\{a,b,d\}}+e_{\{a,c,d\}}-e_{\{a,b,c,d\}}
\\=e_{\{a\}}-3e_{\{a,b\}}+3e_{\{a,b,c\}}-e_{\{a,b,c,d\}}\\={\left(\frac34\right)}^4-3\cdot{\left(\frac24\right)}^4+3\cdot{\left(\frac14\right)}^4-0=\frac9{64}.$
By symmetry, the probability $p_{\{x\}}$ that box $x$ is the only empty box is $\frac9{64}$ for each $x$.
The probability you want is $p_{\{a\}}+p_{\{b\}}+p_{\{c\}}+p_{\{d\}}=4\cdot\frac9{64}=\frac9{16}$. (No inclusion-exclusion is needed for this step because no two different boxes can each be the only empty box.)