During nightly jobs the core becomes saturated with nightly processes such as rollups, attachability, delete RPFS and transfer jobs.
Modify all agents protection schedules to allow the core to process nightly jobs without the added load of transfers.
Example: Modify the protection schedule of each machine to only perform transfers between 03:00AM and 11:59PM. This creates a window for the core to process nightly jobs. Set nightly jobs to start at 12:00AM which allows the core 3 hours to complete tasks such as log truncation.
Note: should your backups run nightly then modify the nightly jobs to run so that it does not conflict.