If the backups are being stored on the domain controllers then why is there a significant differe (4290651)

If the backups are being stored on the domain controllers then why is there a significant difference in backup times?

The backup times will differ because even though the backup agent is deployed to the DC to do the backup, the console is still sending controls for the backup process to the agent. In environments with a large amount of SYSVOL files and slow WAN links, it could cause the backup process to take longer as it needs to send a control for each file. This is assuming that the backups are the same size for each DC.