Hi Alan,
Are you working with the release version of mojoPortal or from svn? I think in svn, since the last release I have added some min-height settings in css to fix this. That article you linked is very good, perhaps better than what I've done. When I get a chance maybe I will try and create a new skin based on their template layout, or maybe you can experiment with trying to do that.
You are right that centered1 is different than the other skins, it uses a different technique for achieving the column layout whereas most other skins use absolute positioning for the left and right columns and margins for the middle. The issue you mention is caused by use of absolute postion. The middle column doesn't know about the position of the left and right side since they are taken out of document flow. Min-height fixed it to some extent.
Cheers,
Joe