I’m not sure where it came from but I saw it on IRC, around the same time ICQ, msn, and aim were in their heyday.

And that makes sense, I’ve never used a teletype system and guess that especially the old ones might have had difficulty generating the correct rise in tone to signal a question, especially if it does text to voice on the fly while things are being typed and might already be saying the word that needs to be said differently to imply a question.