This problem will occur using the generic design of nopcommerce theme. The min-height property will also not work accurately. You would have to make some design level changes like rework the div nesting etc.
1. Make a div that starts before master-wrapper-leftside-3 and ends after master-wrapper-rightside-3 (be sure to add a clear: both; before the </div> to stop it collapsing!) and define a background image with your 2 columns in it. So it'll be 950px x 1px or whatever the width is. This means that the bg image will always expand to the deepest column and give the impression that the other 2 columns are the same size.
2. Find a 'equal columns' javascript. There are a few out there.