I can't use the "Fixed size" radio button to adjust bar widths.

This is a known bug in Prism 3. The button works for bar graphs, but not for column graphs.

Actually, the fixed width option is usually more of a distraction than helpful, as it then requires you to fuss with the width of the graph itself, to show all the columns and not leave much blank space.

You can probably get the effect you want by adjusting the percent gap between columns and by dragging the graph axis to make the graph wider. The width of each column (or box, in the case of box-and-whickers graphs) is determined by the number on the graph, the width of the graph, and the percent gap between columns. You probably don't want to change the number of data sets on the graph, but you can change the width of the graph and the percent gap, and this gives you complete control.

To avoid confusion, we removed the option to use fixed-size columns from Prism 4. Read more about adjusting the width of columns on a graph here.