This looks like a bug triggered by the Page Break separator; from a cursory look I’m not sure why, but the empty line coming out of compile is attached to that section break in the RTF/DOCX formats. I haven’t at the moment found a good workaround for this within Scrivener, but you should at least be able to make quick work of cleaning up the unwanted lines in Word using the advanced Find/Replace there.
Search for ^b^p (wildcards for a section break followed by a paragraph mark) and then replace it with ^m (manual page break). Click the More>> button to see the full search options so you can set the search scope to “Down”, place the insertion point at the start of your text, and then use Replace All. (Setting the scope this way seems to avoid the footer getting caught up in the search/replace, although in my test Word would just pop up a warning that it couldn’t do the replacement there and then would proceed with the rest of the replacements.) That should get you the page breaks with the title starting at the top as intended.