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Yes, the reader makes a difference to how the file appears. The same epub file will look different depending on the reader and the settings. I haven't had a problem with different spacing between paragraphs though. It sounds like a formatting error. If the paragraphs aren't consistent, I'd say you go back to your word doc and select all. Then go to Format --> Paragraph and choose a first line indent or a trailing space.
If you've already done that, then I have no idea.
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