Delay between backup started and scanning filesystem

I have a backup job set to start automatically, which all seems fine, but in the backup logs I am seeming to get massive delays between when the job “starts” and when it begins looking for changes on the drives:

Level Time Message
Info 06/08/18 00:23 Starting scheduled incremental file backup...
Info 06/08/18 02:48 Scanning for changed hard links on volume of "e:\"...

Previously the scanning step would be pretty much instant after the message saying it’s started.

Does anyone know what may be causing this?