To my linguist friends: Doug Hoylman asks, "Why does everyone pronounce this game [Chrononauts] as though it started with 'crow'? Every other English word starting with 'chron'—chronology, chronicle, chronometer, chronic—has a short o." I can't think of a good reason, yet I also pronounce it with a long o. Might it be due to the secondary emphasis on the last syllable? The word chronon is pronounced with a long o as well, but I'm not sure that has common enough usage to matter (and it leads to its own pronunciation question).
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m-w says chronogram and chronograph can both be pronounced that way, which fits with your secondary emphasis idea.