Interesting, I just licence enabled one of these user accounts so I could open their mailbox in Outlook Web App. There mailbox does have recent emails, and appears to be up to date.
So it looks like the messages in these log files are maybe a little misleading, or at the very least confusing.
It looks like incremental syncs are actually working, but regularly get connection errors and generate the error message in the log files. But the syncs are still continuing again on retrys.
So it looks like I've misunderstood these logs and the incremental syncs are actually working.
Oh for the day Microsoft provides clear and useful error messages lol!
Surely though Jason you should have known this ;)