I have a similar problem (in a way).
I have the footer displaying correctly, but the problem is with my wrapper/container div.
I have 2 divs, one on left with variable height content and one on right which is fixed height. Sometimes left div is longer than right div and sometimes it isnt. The problem is that the wrapper div that goes around these 2 divs does not display properly when trying to use height of either 'auto' or '100%'. The wrapper div just doesn't show. If I choose a specific height for the wrapper div it displays like I would like it to, but I need the length variable in case left div becomes large.
Any suggestions welcome.