Hi Nick,
UpdraftPlus uses the standard WordPress hooks to detect when an automatic update is triggered. I’m afraid that we do not have much expertise with JetPack, so it may be that the JetPack AutoUpdate module uses a different mechanism to trigger updates.
If so, this would prevent UpdraftPlus from detecting when an update is about to happen.
I would recommend opening a thread on the JetPack forums asking about the issue. They are very responsive and should be able to provide more information about how JetPack handles these updates.
Best Wishes,
David N