being off by an entire minute would be an obvious problem

It does not have to be off by an entire minute to cause this type of problem. A few milliseconds would be enough if the code we see is only run once per minute to check if any emails should be sent. If I understand correctly, between greater timing accuracy and a more efficient scheduler, the code could be seeing "10.03" minutes in Windows and "9.97" minutes (then "10.96" when the email is sent "11 minutes later") in Linux.