Here's a weird thing. Try type a single character of the box glyph somewhere on the page and send it to the back. Then try it again.
I do remember dealing with this issue back in the olddd (CS3??) days, where glyphs used specifically as bullet list characters (but not elsewhere) sometime encoded differently than the font's native encoding (Always hex:1D (decimal 29) off and this seems to be happening here. your box should be hex0063 but is encoding as hex0046, which is exactly 1D.) so maybe an old issue has resurfaced?
That being said, it's not uncommon for subset fonts (e.g. XXXXXX+Webdings), especialy CID encoded ones, to totally rewrite their own encoding for the purposes of printing the PDF. But when you want to do something else with it, like open them in Illustrator, it's not a recommended practice at the best of times, and weird font encodings is up there on the list.
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