Yeah, that's my whole point behind needing the testing tool as having to publish then unpublish is just stupid. That shouldn't be needed. If something like Sigil or Calibre could give the exact same output as Smashword's own system, then that'd be a whole other ball of wax. But last I checked you can't import a doc file into Sigil and Calibre doesn't convert the file the same as Smashwords.
Of course, something you might try to discover the issues is to take the sections that are having issues, cut out everything from above the troubled area down to below it, then paste that into a raw text editor. I'm thinking something like Notepad on Windows, or Kwrite on Linux. Save, exit, reopen. That'll strip the text down to raw Ascii without any residual code left over. Then cut and paste that back into the document and reapply the formatting tweaks.
It's a bit of a round about way to solve your issue, but it's worked for me whenever I've had lots of seemingly unfixable erroneous formatting issues. You also might need to translate it into Open Document in Open Office first to fix the issue (MS Word is notorious for formatting issues and corruption of the file) before converting back into an MS Word Doc.