The task that settles transactions runs once a day. By default it runs at 4 AM. When you have a sync that is scheduled to run daily, it's helpful for the settlement task to finish running before your sync. If that doesn't happen, then you won't get all of the transactions until the next day.
This can be fixed one of two ways: 1) the sync schedule can be pushed forward or 2) your settlement task can be pushed backward. The down side of pushing the sync forward is that if it is pushed too far forward, it may still be running during the business day when the servers have a heavier load slowing your sync down. The down side of pushing the settlement task backward depends on you payment processor. Some payment processors only have settlement data available after a certain time every morning where as some payment processors have settlement data more frequently. Contact support if you would like to look into either of these options as these are not changes you can make.