So this is how I ended up getting the values to square up including setting the RangeAxis range dynamically. I also removed the 3d elements on suggestion of @FredK. I am using a DefaultCategoryDataSet (plot is a CategoryPlot), so the code below is appropriate for these conditions...
LogAxis yAxis = new LogAxis("Transaction Time (ms)");
yAxis.setBase(10);
plot.setRangeAxis(yAxis);
yAxis.setTickUnit(new NumberTickUnit(1));
yAxis.setMinorTickMarksVisible(true);
yAxis.setAutoRange(true);
plot.setRangeAxis(yAxis);
plot.getRangeAxis().setLabelFont(new Font("SansSerif", Font.BOLD, 14));
plot.getRangeAxis().setTickLabelFont(new Font("SansSerif", Font.BOLD, 12));
Double maximum = (Double) DatasetUtilities.findMaximumRangeValue(dataset);
plot.getRangeAxis().setLowerBound(10);
plot.getRangeAxis().setUpperBound(maximum * 1.6);