The problem is that it seems that the portlets (stylized divs) do not have any, I guess you would call it "weight". For instance the footer completely passes under the portlets. Sorry I don’t have an example because it is in a secure web app. How do I fix this?
Weirdly enough I just upgraded to wordpress 3 and noticed that the dashboard is exactly what I am going for. It uses jquery ui and everything. I am using the 960px framework. Below is a pic of the problem. If you need the code I’ll just move it to its own page.