Do you have a link that we can work with?
I'm guessing that your problem is that you are setting divs to height:100% and css doesn't work like that. Read the css faq on 100% height as it's an important concept.
You can't set 100% height on an element unless its parent has a height defined (i.e. a height not defined by its content and not height:auto). If the parent has a height set (e.g. 500px) then you could set the inner element to height:100% and it would work for a little while. However as soon as the inner content reaches the 100% mark then it breaks out because 100% is a fixed height and cannot grow.
Only tables (or display:table) allows you set a height and then allow content to exceed that height if needed.
You cannot simply make equal column in CSS by using 100% height. There are faux column methods (and overlay methods) that can do this or for modern browsers (IE8+) you can use display:table properties.
I'd need to see the page/design to offer an alternative.