I don't know about the centering issue, but I found that my extra line spacing "disappeared" when converting sometimes, too. I "fixed" it by changing the empty lines' from having paragraph returns (^p) to line endings (^l). It wasn't necessary to replace all paragraph returns, just the ones where I wanted a blank line.
HTH.
Edited: What I did was search & replace: ^p^p with ^p^l
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