This is my first feedback so please forgive if I've misunderstood but I solved this issue with a simpler explanation (at least for me).
boxplot plots each columns as a separate variable (box) as long as the lengths of each column are the same.
I simply created a NaN matrix with number of rows equal to the length of my longest variable, then populated with my variable data. The NaNs are not plotted on the box plot but allows variables of unequal length to be plotted. Also to add more variables, simply increase the number of columns in your NaN array.
I hope this helps anyone returning to this thread :)