If you are using Kentico 9 - there was, regrettably a bug. So, maybe this is the cause. It was fixed in 9.0.10 hotfix:
"Scheduler - Infinite loop when planning the next run time of scheduled tasks in rare cases Planning of the next run time for scheduled tasks resulted in an infinite loop in rare cases. This could cause very high CPU usage on the server."
This bug occurred mostly around midnight - so, maybe it is preventing the other tasks from being executed too.