With the newest version of CSS Sculptor you should be able to check the box for equal column lengths in the interface to have it make them the same length. I tested this in FireFox 3.5.3 and was able to confirm that it seems to be working correctly.
Are you using the newest CSS Sculptor v3? Please post back and let us know what version and layout you are working with so we can help determine what is going on. If you have a link or a screen shot that would also be helpful.