The issue is by design as queued jobs that do not have the time of being started (and executed) during the backup period are dropped so the network load is reduced.
This RapidRecovery 6.0.x behavior differs from the one in AppAssure 5.4.x. The change has been introduced to minimize the number of backup jobs executed outside the backup window.
The solution for avoiding the errors is changing the end time of the backup Window.
For instance, using the example above with multiple machines protected on an hourly schedule and the backup window ending at 11PM, the solution is changing the end of the backup interval either to 10:59PM so the last backups are started at 10PM or to 11:59 so the last backups for the interval are started at 11PM.
Based on your environment specifics there are other possible variations but the objective is the same: allowing enough time for all the last backups of the interval to run.