I think the box plots were a good choice here. I quickly understood what I was looking at, which is a high compliment for any visualization. When it's done right it seems easy and obvious.
But the y-axis really needs to start at 0. It's the only way the reader will perceive the correct relative difference between the various measurements.
As an extreme example, if I have measurements [A: 100, B: 101, C: 105], and then scale the axes to "fit around" the data (maybe from 100 to 106 on thy y axis), it will seem like C is 5x larger than B. In reality, it's only 1.05x larger.
Leave the whitespace at the bottom of the graph if the relative size of the measurements matters (it usually does).