Well, I figured out what was causing the black boxes for carriage returns. Apparently I added a blank glyph in Inkscape and when the font was translated to TrueType, the blank glyph got mapped to CR. I was able to use FontForge to delete it. (I couldn't find any way to delete it in Inkscape.) So, maybe that will save someone some trouble in the future.

(Incidentally, fonts are much more complicated than I would have guessed.)