Do normal offline messages get stored in the Offline messages store (when you log off normally and someone sends a message to you)? If yes, then there is nothing you can do more.
This issue is very old, older than 3.7.1 version, i'm using that system property for 6 years maybe. You probably haven't noticed this before. Or some changes to sessions management between 3.7.1 and 3.9.3 had made it to appear more often.
There is no mechanism in Openfire to handle that. There is "XEP-0184: Message Delivery Receipts" protocol. But it's a client side protocol. A client should have support for that. Smack library has it, but Spark doesn't. This protocol sends additional delivery receipts with a message and waits for an acknowledgment from another client that a message has been received. Client has to have some GUI interface for that, to show which messages have been received and which not.
Another mechanism is "XEP-0198: Stream Management", which is server side (
OF-446), but i see that client also needs to support that. Smack library supports that already (not sure what should be done to make Spark support that), but Openfire doesn't.
Until one (or both) of this mechanisms is implemented, you don't have any options to ensure a message always goes to a recipient. That system property is the only thing you can do. Do some testing and find which value is low enough and is comfortable for your network.