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A backup performed within Rescue does not use VSS, and some VSS writers in Windows will remove data from the snapshot. For example, previous VSS snapshots are not included, and Windows Search deletes its indexing database from snapshots because it can grow quite large and is automatically rebuilt when missing anyway. If you look at the logs from a job performed in Windows and a job performed in Rescue, you may find that the former includes less source data than the latter, or of course just compare the size of the generated backup files.
The other (or additional) factor could be that WinPE defaults to the “Balanced” power profile, not “High Performance”. To change that, copy this into a text file that you store your flash drive or something to make it easier, then before starting a backup, open Command Prompt from the Rescue Media taskbar and enter this:
powercfg /s 8c5e7fda-e8bf-4a96-9a85-a6e23a8c635c