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if what's happening is that the columns go crazy and everything below the header resizes to different widths depending on the content displayed. This has ocurred to me before when there is a colspan somewhere inside the main table / container of the theme, that happens when creating a theme you select some cells and merge them. Usually the table where the code of the blocks and $content is should be left untouched and you place the header and footer in a table/div above and below the main container, that has been a solution that has worked for me so far. When this has happened to me it looks ok in Firefox and bad in IE, but yours is looking bad in FF too, so I don't know if this solution would apply in this case too.