Center content pushed down when no right column blocks (main.tpl central.tpl)

We are evaluating running 2.0.14. We created some a custom skin. We are running into an issue that when we go into Admin > Design > Blocks > Pages and disable all the right column blocks, the page content in the center is pushed down so it starts at the bottom of the left column. We though it was an issue with the skin, but we changed back to the Basic skin and have the same issue.

Any help with troubleshooting is greatly appreciated. We really like this software!