I'm probably going to get massive downvotes for this, but those little boxes, in my experience, mean that there are no glyphs associated with the character codes. (added in edit) Incorrect end-of-line markers (end of addition) That typically result in the text being squished onto one line; if you're "flooded with little squares" I don't think that the problem is the end-of-line markers.
Have you tried a) changing the font in Notepad, so see if the little boxes go away, b) opening the document in another editor see if the problem is unique to Notepad or c) explicitly creating the document in UTF-8?
Edited to make the 2d sentence comprehensible
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