I don't know if this is still true but some word processing programs would insert a "different" space character if you held down the ctl (control) key when you tapped the space bar. So I'm wondering if the space you see is some sort of different space character.
Along those lines, in Calibre's Convert window, under Look & Feel, in the Text tab, there's a check box, Transliterate unicode characters to ASCII; maybe try turning that on and see if it helps.
Or, did you try Sigil's Mend and prettify all html files? Calibre also has the same thing.
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