I was thinking something like that - but disabling the 'Beta: Use Unicode UTF-8 for worldwide language support' didn't work (and though I can't completely rely on my memory, I don't think I've ever changed it previously).
I did find one thing that may be a clue: if I paste in a Unicode character from
BabelMap, it produces the notdef glyph. If I type it in manually with the numpad or copy from Windows Charmap, it works.
I've sent an email to the developer of BabelMap to see if they have any idea of why it's different; hopefully that'll give me some idea of whats going on.