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It sounds like you have some defined-size text frames in the document and the export process is unable to maintain the definition. Since reflowable essentially disposes with the whole text containment (pages and frames) it should have no effect on the result.
I'd go through the document and see if an Object Style is applied to any of the text frames (especially an overrride on one or two), or just reflow the content into a new, clean ID document, and see what happens.
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