In the new Program Beta experience, the Program is scheduled to run at a time independent of the sync of the list of Participants. These should be chained, similar to the existing Program where the active Program is always looking for new participants and sending emails. According to this ticket 29653, the new Programs only run at a fixed time set in the Program settings and the Data Designer or any other dependency may not have completed syncing the current information.
Ideally, this enhancement would allow participants to join a program more often than once per day.
We have some messages where we are trying to drive a client action within 48 hours, and with the timing of the syncs and the Program only running once per day, there is a chance they will not receive our email until after the time we are driving an action to happen.