The Equal columns setting uses a 2px high background image to create an illusion.
the columns themselves are not equal, but the background image which includes the colors and borders of the column layout creates the illusion of the shorter column extending to be the same length as the longer column.
in reality the shorter column is still shorter, but the end user cant see it.
perhaps it would make more sense if you viewed the equal column layout in Fire Fox with the Firebug extension installed. With fire bug you can edit the css in real time, you could disable the faux columns background image to see what the design looks like, then toggle it back on to see what the effect is doing.
see this article for more details: