it depends 100% on the scripts the theme (or your plugins) use. Sometimes some scripts conflict with others, the best way to avoid this is to use all jquery, or all scriptaculous or all mootools or whatever. Do a search for jquery noconflict and you'll find a non-conflict version that solves this kind of problems MOST of the times (not always)
bah, don't search anything, just go here
Of course, you could use another theme if the above doesn't solve things.
Another possibility is that you may have CSS styles overriden by some script, check out if you have CSS elements declared twice (in the same or different stylesheets)
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