it's known upgrade issue with obsolete table-based layout themes.
Please see http://themes.tikiwiki.org/Theme+Issues+when+Updating+to+Tiki3.0
You have two options:
- modify the theme templates/styles/themename/ tiki.tpl and header.tpl (if any) to be tableless and Tiki 3 compatible and import lite/lite.css on top of the theme stylesheet
- select another theme from the new ones for your site