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Apache won't render it differently. If the HTML source matches in both locations, this isn't a PHP issue, its a rendering one so its your HTML and CSS that's at fault.
There are a lot of things different between these two servers setups. I haven't a clue what the differences between the Zend application are, but 5.3 and 5.2 have many differences (albeit most are object oriented and 5.3 is mostly backwards compatible with the exception of namespaces and constructors if they match the class names).
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