Exactly what sort of objects are you asking about? That is, what tool did you use to add the square? If it's a markup (annotation), you can use the TouchUp object tool to rotate it if you flatten it so it's part of the regular page contents. Here's a link to a handy free JavaScript-based tool that lets you selectively flatten annotations: UVSAR : Selective Flattener tool for Adobe Acrobat 8, 9 and X
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