I have come across this problem of character encoding a couple of times in the last year, it seems, as far as I can tell, not to be a function of text cleaner but something in the original file. It seems that some Microsoft software is not applying the correct coding and this error propagates into other systems getting confused and trying to re-encode. The main problem seems to be Libre(or Open)Office trying to correct errors in Word. Without being biased it seems that many US Windows installs are not Internationally aware.
Have you tried the other suggestion of using Calibre to convert to html first? This should solve the encoding issue and if the linefeeds are still there text cleaner should just remove them.
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