I don't think that the code has changed at all in a way that affects this. (The way the functionality is described in the docs may have been.) It has always been like that.
It may be that your server is getting progressively more heavily loaded, and so it is now taking more than 60 seconds from when the time expires on the student's computer until the server processes the submission, but that is a guess.
Quiz
Timed Quiz Penalty
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