Inconsistency regarding "System Batches" during upgrades

I'm wondering if anyone has the inside scoop on "System Batches" during upgrades.

Sometimes the upgrade procedure will stop and prompt you to deal with open "System Batches" resulting from open invoices, and other times it does not.  I have seen inconsistency in this process.  It would of course be better if it were consistent so that we could expect that what we will see when upgrading production systems would be the same behavior we saw during testing.